Local-scale urban meteorological parameterization scheme (LUMPS): longwave radiation parameterization and seasonality-related developments

Recent developments to the Local-scale Urban Meteorological Parameterization Scheme (LUMPS), a simple model able to simulate the urban energy balance, are presented. The major development is the coupling of LUMPS to the Net All-Wave Radiation Parameterization (NARP). Other enhancements include that the model now accounts for the changing availability of water at the surface, seasonal variations of active vegetation, and the anthropogenic heat flux, while maintaining the need for only commonly available meteorological observations and basic surface characteristics. The incoming component of the longwave radiation (L↓) in NARP is improved through a simple relation derived using cloud cover observations from a ceilometer collected in central London, England. The new L↓ formulation is evaluated with two independent multiyear datasets (Łódź, Poland, and Baltimore, Maryland) and compared with alternatives that include the original NARP and a simpler one using the National Climatic Data Center cloud observation database as input. The performance for the surface energy balance fluxes is assessed using a 2-yr dataset (Łódź). Results have an overall RMSE < 34 W m−2 for all surface energy balance fluxes over the 2-yr period when

A multi-instrument comparison of integrated water vapour measurements at a high latitude site

We compare measurements of integrated water vapour (IWV) over a subarctic site (Kiruna, Northern Sweden) from five different sensors and retrieval methods: Radiosondes, Global Positioning System (GPS), ground-based Fourier-transform infrared (FTIR) spectrometer, ground-based microwave radiometer, and satellite-based microwave radiometer (AMSU-B). Additionally, we compare also to ERA-Interim model reanalysis data. GPS-based IWV data have the highest temporal coverage and resolution and are chosen as reference data set. All datasets agree reasonably well, but the ground-based microwave instrument only if the data are cloud-filtered. We also address two issues that are general for such intercomparison studies, the impact of different lower altitude limits for the IWV integration, and the impact of representativeness error. We develop methods for correcting for the former, and estimating the random error contribution of the latter. A literature survey reveals that reported systematic differences between different techniques are study-dependent and show no overall consistent pattern. Further improving the absolute accuracy of IWV measurements and providing climate-quality time series therefore remain challenging problems.

GDASH: a grid-enabled program for structure solution from powder diffraction data

The simulated annealing approach to structure solution from powder diffraction data, as implemented in the DASH program, is easily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can therefore be achieved by distributing individual DASH runs over a network of computers. The GDASH program achieves this by packaging DASH in a form that enables it to run under the Univa UD Grid MP system, which harnesses networks of existing computing resources to perform calculations.

Evaluation of ice cloud representation in the ECMWF and UK Met Office models using CloudSat and CALIPSO data

Ice cloud representation in general circulation models remains a challenging task, due to the lack of accurate observations and the complexity of microphysical processes. In this article, we evaluate the ice water content (IWC) and ice cloud fraction statistical distributions from the numerical weather prediction models of the European Centre for Medium-Range Weather Forecasts (ECMWF) and the UK Met Office, exploiting the synergy between the CloudSat radar and CALIPSO lidar. Using the last three weeks of July 2006, we analyse the global ice cloud occurrence as a function of temperature and latitude and show that the models capture the main geographical and temperature-dependent distributions, but overestimate the ice cloud occurrence in the Tropics in the temperature range from −60 °C to −20 °C and in the Antarctic for temperatures higher than −20 °C, but underestimate ice cloud occurrence at very low temperatures. A global statistical comparison of the occurrence of grid-box mean IWC at different temperatures shows that both the mean and range of IWC increases with increasing temperature. Globally, the models capture most of the IWC variability in the temperature range between −60 °C and −5 °C, and also reproduce the observed latitudinal dependencies in the IWC distribution due to different meteorological regimes. Two versions of the ECMWF model are assessed. The recent operational version with a diagnostic representation of precipitating snow and mixed-phase ice cloud fails to represent the IWC distribution in the −20 °C to 0 °C range, but a new version with prognostic variables for liquid water, ice and snow is much closer to the observed distribution. The comparison of models and observations provides a much-needed analysis of the vertical distribution of IWC across the globe, highlighting the ability of the models to reproduce much of the observed variability as well as the deficiencies where further improvements are required.

Grid warehousing of molecular dynamics protein unfolding data

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding ways to enhance performance is a grid issue on its own. However, more and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. This paper describes efforts to provide a grid-enabled data warehouse for protein unfolding data. We outline the challenge and present first results in the design and implementation of the data warehouse.

Grid computing solutions for distributed repositories of protein folding and unfolding simulations

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data and a data warehouse. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular we look at two aspects, first how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories --- this is an important and challenging aspect of P-found because the data volumes involved are too large to be centralised. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling new scientific discoveries.

Pragmatic oriented data interoperability for smart healthcare information systems

Smart healthcare is a complex domain for systems integration due to human and technical factors and heterogeneous data sources involved. As a part of smart city, it is such a complex area where clinical functions require smartness of multi-systems collaborations for effective communications among departments, and radiology is one of the areas highly relies on intelligent information integration and communication. Therefore, it faces many challenges regarding integration and its interoperability such as information collision, heterogeneous data sources, policy obstacles, and procedure mismanagement. The purpose of this study is to conduct an analysis of data, semantic, and pragmatic interoperability of systems integration in radiology department, and to develop a pragmatic interoperability framework for guiding the integration. We select an on-going project at a local hospital for undertaking our case study. The project is to achieve data sharing and interoperability among Radiology Information Systems (RIS), Electronic Patient Record (EPR), and Picture Archiving and Communication Systems (PACS). Qualitative data collection and analysis methods are used. The data sources consisted of documentation including publications and internal working papers, one year of non-participant observations and 37 interviews with radiologists, clinicians, directors of IT services, referring clinicians, radiographers, receptionists and secretary. We identified four primary phases of data analysis process for the case study: requirements and barriers identification, integration approach, interoperability measurements, and knowledge foundations. Each phase is discussed and supported by qualitative data. Through the analysis we also develop a pragmatic interoperability framework that summaries the empirical findings and proposes recommendations for guiding the integration in the radiology context.

CDASH: a cloud-enabled program for structure solution from powder diffraction data

The simulated annealing approach to crystal structure determination from powder diffraction data, as implemented in the DASH program, is readily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can be achieved by distributing individual DASH runs over a network of computers. The CDASH program delivers this by using scalable on-demand computing clusters built on the Amazon Elastic Compute Cloud service. By way of example, a 360 vCPU cluster returned the crystal structure of racemic ornidazole (Z0 = 3, 30 degrees of freedom) ca 40 times faster than a typical modern quad-core desktop CPU. Whilst used here specifically for DASH, this approach is of general applicability to other packages that are amenable to coarse-grained parallelism strategies.

Tripleclouds: an efficient method for representing horizontal cloud inhomogeneity in 1D radiation schemes by using three regions at each height

Radiation schemes in general circulation models currently make a number of simplifications when accounting for clouds, one of the most important being the removal of horizontal inhomogeneity. A new scheme is presented that attempts to account for the neglected inhomogeneity by using two regions of cloud in each vertical level of the model as opposed to one. One of these regions is used to represent the optically thinner cloud in the level, and the other represents the optically thicker cloud. So, along with the clear-sky region, the scheme has three regions in each model level and is referred to as “Tripleclouds.” In addition, the scheme has the capability to represent arbitrary vertical overlap between the three regions in pairs of adjacent levels. This scheme is implemented in the Edwards–Slingo radiation code and tested on 250 h of data from 12 different days. The data are derived from cloud retrievals using radar, lidar, and a microwave radiometer at Chilbolton, southern United Kingdom. When the data are grouped into periods equivalent in size to general circulation model grid boxes, the shortwave plane-parallel albedo bias is found to be 8%, while the corresponding bias is found to be less than 1% using Tripleclouds. Similar results are found for the longwave biases. Tripleclouds is then compared to a more conventional method of accounting for inhomogeneity that multiplies optical depths by a constant scaling factor, and Tripleclouds is seen to improve on this method both in terms of top-of-atmosphere radiative flux biases and internal heating rates.

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.

Evaluation of a large-eddy model simulation of a mixed-phase altocumulus cloud using microwave radiometer, lidar and Doppler radar data

Using the Met Office large-eddy model (LEM) we simulate a mixed-phase altocumulus cloud that was observed from Chilbolton in southern England by a 94 GHz Doppler radar, a 905 nm lidar, a dual-wavelength microwave radiometer and also by four radiosondes. It is important to test and evaluate such simulations with observations, since there are significant differences between results from different cloud-resolving models for ice clouds. Simulating the Doppler radar and lidar data within the LEM allows us to compare observed and modelled quantities directly, and allows us to explore the relationships between observed and unobserved variables. For general-circulation models, which currently tend to give poor representations of mixed-phase clouds, the case shows the importance of using: (i) separate prognostic ice and liquid water, (ii) a vertical resolution that captures the thin layers of liquid water, and (iii) an accurate representation the subgrid vertical velocities that allow liquid water to form. It is shown that large-scale ascents and descents are significant for this case, and so the horizontally averaged LEM profiles are relaxed towards observed profiles to account for these. The LEM simulation then gives a reasonable. cloud, with an ice-water path approximately two thirds of that observed, with liquid water at the cloud top, as observed. However, the liquid-water cells that form in the updraughts at cloud top in the LEM have liquid-water paths (LWPs) up to half those observed, and there are too few cells, giving a mean LWP five to ten times smaller than observed. In reality, ice nucleation and fallout may deplete ice-nuclei concentrations at the cloud top, allowing more liquid water to form there, but this process is not represented in the model. Decreasing the heterogeneous nucleation rate in the LEM increased the LWP, which supports this hypothesis. The LEM captures the increase in the standard deviation in Doppler velocities (and so vertical winds) with height, but values are 1.5 to 4 times smaller than observed (although values are larger in an unforced model run, this only increases the modelled LWP by a factor of approximately two). The LEM data show that, for values larger than approximately 12 cm s(-1), the standard deviation in Doppler velocities provides an almost unbiased estimate of the standard deviation in vertical winds, but provides an overestimate for smaller values. Time-smoothing the observed Doppler velocities and modelled mass-squared-weighted fallspeeds shows that observed fallspeeds are approximately two-thirds of the modelled values. Decreasing the modelled fallspeeds to those observed increases the modelled IWC, giving an IWP 1.6 times that observed.

Results from the CERN pilot CLOUD experiment

During a 4-week run in October–November 2006, a pilot experiment was performed at the CERN Proton Synchrotron in preparation for the Cosmics Leaving OUtdoor Droplets (CLOUD) experiment, whose aim is to study the possible influence of cosmic rays on clouds. The purpose of the pilot experiment was firstly to carry out exploratory measurements of the effect of ionising particle radiation on aerosol formation from trace H2SO4 vapour and secondly to provide technical input for the CLOUD design. A total of 44 nucleation bursts were produced and recorded, with formation rates of particles above the 3 nm detection threshold of between 0.1 and 100 cm−3 s−1, and growth rates between 2 and 37 nm h−1. The corresponding H2SO4 concentrations were typically around 106 cm−3 or less. The experimentally-measured formation rates and H2SO4 concentrations are comparable to those found in the atmosphere, supporting the idea that sulphuric acid is involved in the nucleation of atmospheric aerosols. However, sulphuric acid alone is not able to explain the observed rapid growth rates, which suggests the presence of additional trace vapours in the aerosol chamber, whose identity is unknown. By analysing the charged fraction, a few of the aerosol bursts appear to have a contribution from ion-induced nucleation and ion-ion recombination to form neutral clusters. Some indications were also found for the accelerator beam timing and intensity to influence the aerosol particle formation rate at the highest experimental SO2 concentrations of 6 ppb, although none was found at lower concentrations. Overall, the exploratory measurements provide suggestive evidence for ion-induced nucleation or ion-ion recombination as sources of aerosol particles. However in order to quantify the conditions under which ion processes become significant, improvements are needed in controlling the experimental variables and in the reproducibility of the experiments. Finally, concerning technical aspects, the most important lessons for the CLOUD design include the stringent requirement of internal cleanliness of the aerosol chamber, as well as maintenance of extremely stable temperatures (variations below 0.1 _C).