A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

Evaluating the ability of a numerical weather prediction model to forecast tracer concentrations during ETEX 2

In this paper the meteorological processes responsible for transporting tracer during the second ETEX (European Tracer EXperiment) release are determined using the UK Met Office Unified Model (UM). The UM predicted distribution of tracer is also compared with observations from the ETEX campaign. The dominant meteorological process is a warm conveyor belt which transports large amounts of tracer away from the surface up to a height of 4 km over a 36 h period. Convection is also an important process, transporting tracer to heights of up to 8 km. Potential sources of error when using an operational numerical weather prediction model to forecast air quality are also investigated. These potential sources of error include model dynamics, model resolution and model physics. In the UM a semi-Lagrangian monotonic advection scheme is used with cubic polynomial interpolation. This can predict unrealistic negative values of tracer which are subsequently set to zero, and hence results in an overprediction of tracer concentrations. In order to conserve mass in the UM tracer simulations it was necessary to include a flux corrected transport method. Model resolution can also affect the accuracy of predicted tracer distributions. Low resolution simulations (50 km grid length) were unable to resolve a change in wind direction observed during ETEX 2, this led to an error in the transport direction and hence an error in tracer distribution. High resolution simulations (12 km grid length) captured the change in wind direction and hence produced a tracer distribution that compared better with the observations. The representation of convective mixing was found to have a large effect on the vertical transport of tracer. Turning off the convective mixing parameterisation in the UM significantly reduced the vertical transport of tracer. Finally, air quality forecasts were found to be sensitive to the timing of synoptic scale features. Errors in the position of the cold front relative to the tracer release location of only 1 h resulted in changes in the predicted tracer concentrations that were of the same order of magnitude as the absolute tracer concentrations.

On differentiating ground clutter and insect echoes from Doppler weather radars using archived data

Normally wind measurements from Doppler radars rely on the presence of rain. During fine weather, insects become a potential radar target for wind measurement. However, it is difficult to separate ground clutter and insect echoes when spectral or polarimetric methods are not available. Archived reflectivity and velocity data from repeated scans provide alternative methods. The probability of detection (POD) method, which maps areas with a persistent signal as ground clutter, is ineffective when most scans also contain persistent insect echoes. We developed a clutter detection method which maps the standard deviation of velocity (SDV) over a large number of scans, and can differentiate insects and ground clutter close to the radar. Beyond the range of persistent insect echoes, the POD method more thoroughly removes ground clutter. A new, pseudo-probability clutter map was created by combining the POD and SDV maps. The new map optimised ground clutter detection without removing insect echoes.

A comparison of space weather analysis techniques used to predict the arrival of the Earth-directed CME and its shockwave launched on 8 April 2010

The Earth-directed coronal mass ejection (CME) of 8 April 2010 provided an opportunity for space weather predictions from both established and developmental techniques to be made from near–real time data received from the SOHO and STEREO spacecraft; the STEREO spacecraft provide a unique view of Earth-directed events from outside the Sun-Earth line. Although the near–real time data transmitted by the STEREO Space Weather Beacon are significantly poorer in quality than the subsequently downlinked science data, the use of these data has the advantage that near–real time analysis is possible, allowing actual forecasts to be made. The fact that such forecasts cannot be biased by any prior knowledge of the actual arrival time at Earth provides an opportunity for an unbiased comparison between several established and developmental forecasting techniques. We conclude that for forecasts based on the STEREO coronagraph data, it is important to take account of the subsequent acceleration/deceleration of each CME through interaction with the solar wind, while predictions based on measurements of CMEs made by the STEREO Heliospheric Imagers would benefit from higher temporal and spatial resolution. Space weather forecasting tools must work with near–real time data; such data, when provided by science missions, is usually highly compressed and/or reduced in temporal/spatial resolution and may also have significant gaps in coverage, making such forecasts more challenging.

Fair weather atmospheric electricity

Abstract. Not long after Franklin’s iconic studies, an atmospheric electric field was discovered in “fair weather” regions, well away from thunderstorms. The origin of the fair weather field was sought by Lord Kelvin, through development of electrostatic instrumentation and early data logging techniques, but was ultimately explained through the global circuit model of C.T.R. Wilson. In Wilson’s model, charge exchanged by disturbed weather electrifies the ionosphere, and returns via a small vertical current density in fair weather regions. New insights into the relevance of fair weather atmospheric electricity to terrestrial and planetary atmospheres are now emerging. For example, there is a possible role of the global circuit current density in atmospheric processes, such as cloud formation. Beyond natural atmospheric processes, a novel practical application is the use of early atmospheric electrostatic investigations to provide quantitative information on past urban air pollution.

Impact of increasing resolution and a warmer climate on extreme weather from NH extra-tropical cyclones

The effect of a warmer climate on the properties of extra-tropical cyclones is investigated using simulations of the ECHAM5 global climate model at resolutions of T213 (60 km) and T319 (40 km). Two periods representative of the end of the 20th and 21st centuries are investigated using the IPCC A1B scenario. The focus of the paper is on precipitation for the NH summer and winter seasons, however results from vorticity and winds are also presented. Similar number of events are identified at both resolutions. There are, however, a greater number of extreme precipitation events in the higher reso- lution run. The difference between maximum intensity distributions are shown to be statistically significant using a Kolmogorov-Smirnov test. A Generalised Pareto Distribution is used to analyse changes in extreme precipitation and wind events. In both resolutions, there is an increase in the number of ex- treme precipitation events in a warmer climate for all seasons, together with a reduction in return period. This is not associated with any increased verti- cal velocity, or with any increase in wind intensity in the winter and spring. However, there is an increase in wind extremes in the summer and autumn associated with tropical cyclones migrating into the extra-tropics.

Identifying and investigating pesticide application types to promote a more sustainable pesticide use: the case of smallholders in Boyacá, Colombia

The present paper investigates pesticide application types adopted by smallholder potato producers in the Department of Boyacá , Colombia. In this region, environmental, health and adverse economic effects due to pesticide mis- or over-use respectively have been observed. Firstly, pesticide application types were identified based on input-effectiveness. Secondly, their determinants of adoption were investigated. Finally suggestions were given to develop intervention options for transition towards a more sustainable pesticide use. Three application types were identified for fungicide and insecticide. The types differed in terms of input (intensity of pesticide application), effect (damage control), frequency of application, average quantity applied per application, chemical class, and productivity. Then, the determinants of different pesticide application types were investigated with a multinomial logistic regression approach and applying the integrative agent centred (IAC) framework. The area of the plot, attendance at training sessions and educational and income levels were among the most relevant determinants. The analysis suggested that better pesticide use could be fostered to reduce pesticide-related risks in the region. Intervention options were outlined, which may help in targeting this issue. They aim not only at educating farmers, but to change their social and institutional context, by involving other agents of the agricultural system (i.e. pesticide producers), facilitating new institutional settings (i.e. cooperatives) and targeting social dynamics (i.e. conformity to social norms).

Diurnal and seasonal cycles of cloud occurrences, types and radiative impact over West Africa

This study focuses on the occurrence and type of clouds observed in West Africa, a subject which has neither been much documented nor quantified. It takes advantage of data collected above Niamey in 2006 with the ARM mobile facility. A survey of cloud characteristics inferred from ground measurements is presented with a focus on their seasonal evolution and diurnal cycle. Four types of clouds are distinguished: high-level clouds, deep convective clouds, shallow convective clouds and mid-level clouds. A frequent occurrence of the latter clouds located at the top of the Saharan Air Layer is highlighted. High-level clouds are ubiquitous throughout the period whereas shallow convective clouds are mainly noticeable during the core of the monsoon. The diurnal cycle of each cloud category and its seasonal evolution is investigated. CloudSat and CALIPSO data are used in order to demonstrate that these four cloud types (in addition to stratocumulus clouds over the ocean) are not a particularity of the Niamey region and that mid-level clouds are present over the Sahara during most of the Monsoon season. Moreover, using complementary data sets, the radiative impact of each type of clouds at the surface level has been quantified in the shortwave and longwave domain. Mid-level clouds and anvil clouds have the largest impact respectively in longwave (about 15 W m−2) and the shortwave (about 150 W m−2). Furthermore, mid-level clouds exert a strong radiative forcing in Spring at a time when the other cloud types are less numerous.

Advances in continuously profiling the thermodynamic state of the boundary layer: integration of measurements and methods

This paper describes advances in ground-based thermodynamic profiling of the lower troposphere through sensor synergy. The well-documented integrated profiling technique (IPT), which uses a microwave profiler, a cloud radar, and a ceilometer to simultaneously retrieve vertical profiles of temperature, humidity, and liquid water content (LWC) of nonprecipitating clouds, is further developed toward an enhanced performance in the boundary layer and lower troposphere. For a more accurate temperature profile, this is accomplished by including an elevation scanning measurement modus of the microwave profiler. Height-dependent RMS accuracies of temperature (humidity) ranging from 0.3 to 0.9 K (0.5–0.8 g m−3) in the boundary layer are derived from retrieval simulations and confirmed experimentally with measurements at distinct heights taken during the 2005 International Lindenberg Campaign for Assessment of Humidity and Cloud Profiling Systems and its Impact on High-Resolution Modeling (LAUNCH) of the German Weather Service. Temperature inversions, especially of the lower boundary layer, are captured in a very satisfactory way by using the elevation scanning mode. To improve the quality of liquid water content measurements in clouds the authors incorporate a sophisticated target classification scheme developed within the European cloud observing network CloudNet. It allows the detailed discrimination between different types of backscatterers detected by cloud radar and ceilometer. Finally, to allow IPT application also to drizzling cases, an LWC profiling method is integrated. This technique classifies the detected hydrometeors into three different size classes using certain thresholds determined by radar reflectivity and/or ceilometer extinction profiles. By inclusion into IPT, the retrieved profiles are made consistent with the measurements of the microwave profiler and an LWC a priori profile. Results of IPT application to 13 days of the LAUNCH campaign are analyzed, and the importance of integrated profiling for model evaluation is underlined.

Reduced space optimal interpolation of daily rain gauge precipitation in Switzerland

The coarse spacing of automatic rain gauges complicates near-real- time spatial analyses of precipitation. We test the possibility of improving such analyses by considering, in addition to the in situ measurements, the spatial covariance structure inferred from past observations with a denser network. To this end, a statistical reconstruction technique, reduced space optimal interpolation (RSOI), is applied over Switzerland, a region of complex topography. RSOI consists of two main parts. First, principal component analysis (PCA) is applied to obtain a reduced space representation of gridded high- resolution precipitation fields available for a multiyear calibration period in the past. Second, sparse real-time rain gauge observations are used to estimate the principal component scores and to reconstruct the precipitation field. In this way, climatological information at higher resolution than the near-real-time measurements is incorporated into the spatial analysis. PCA is found to efficiently reduce the dimensionality of the calibration fields, and RSOI is successful despite the difficulties associated with the statistical distribution of daily precipitation (skewness, dry days). Examples and a systematic evaluation show substantial added value over a simple interpolation technique that uses near-real-time observations only. The benefit is particularly strong for larger- scale precipitation and prominent topographic effects. Small-scale precipitation features are reconstructed at a skill comparable to that of the simple technique. Stratifying the reconstruction method by the types of weather type classifications yields little added skill. Apart from application in near real time, RSOI may also be valuable for enhancing instrumental precipitation analyses for the historic past when direct observations were sparse.

How to quantify the resolution of surface climate by circulation types: an example for Alpine precipitation

A novel approach is presented for the evaluation of circulation type classifications (CTCs) in terms of their capability to predict surface climate variations. The approach is analogous to that for probabilistic meteorological forecasts and is based on the Brier skill score. This score is shown to take a particularly simple form in the context of CTCs and to quantify the resolution of a climate variable by the classifications. The sampling uncertainty of the skill can be estimated by means of nonparametric bootstrap resampling. The evaluation approach is applied for a systematic intercomparison of 71 CTCs (objective and manual, from COST Action 733) with respect to their ability to resolve daily precipitation in the Alpine region. For essentially all CTCs, the Brier skill score is found to be higher for weak and moderate compared to intense precipitation, for winter compared to summer, and over the north and west of the Alps compared to the south and east. Moreover, CTCs with a higher number of types exhibit better skill than CTCs with few types. Among CTCs with comparable type number, the best automatic classifications are found to outperform the best manual classifications. It is not possible to single out one ‘best’ classification for Alpine precipitation, but there is a small group showing particularly high skill.

Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport

In this study, differences at the genetic level of 37 Salmonella Enteritidis strains from five phage types (PTs) were compared using comparative genomic hybridization (CGH) to assess differences between PTs. There were approximately 400 genes that differentiated prevalent (4, 6, 8 and 13a) and sporadic (11) PTs, of which 35 were unique to prevalent PTs, including six plasmid-borne genes, pefA, B, C, D, srgC and rck, and four chromosomal genes encoding putative amino acid transporters. Phenotype array studies also demonstrated that strains from prevalent PTs were less susceptible to urea stress and utilized L-histidine, L-glutamine, L-proline, L-aspartic acid, gly-asn and gly-gln more efficiently than PT11 strains. Complementation of a PT11 strain with the transporter genes from PT4 resulted in a significant increase in utilization of the amino acids and reduced susceptibility to urea stress. In epithelial cell association assays, PT11 strains were less invasive than other prevalent PTs. Most strains from prevalent PTs were better biofilm formers at 37 degrees C than at 28 degrees C, whilst the converse was true for PT11 strains. Collectively, the results indicate that genetic and corresponding phenotypic differences exist between strains of the prevalent PTs 4, 6, 8 and 13a and non-prevalent PT11 strains that are likely to provide a selective advantage for strains from the former PTs and could help them to enter the food chain and cause salmonellosis.