Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

Modeling dynamical systems represents an important application class covering a wide range of disciplines including but not limited to biology, chemistry, finance, national security, and health care. Such applications typically involve large-scale, irregular graph processing, which makes them difficult to scale due to the evolutionary nature of their workload, irregular communication and load imbalance. EpiSimdemics is such an application simulating epidemic diffusion in extremely large and realistic social contact networks. It implements a graph-based system that captures dynamics among co-evolving entities. This paper presents an implementation of EpiSimdemics in Charm++ that enables future research by social, biological and computational scientists at unprecedented data and system scales. We present new methods for application-specific processing of graph data and demonstrate the effectiveness of these methods on a Cray XE6, specifically NCSA's Blue Waters system.

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.

Transonic Nonlinear Aeroelastic Simulations Using An Harmonic Balance Method

This paper presents an approach to compute transonic Limit Cycle O
scillations using a coupled Harmonic Balance formulation based on the Euler equations for fluid dynamics and finite element models. The paper will investigate the role of aerodynamic (shocks) and structural nonlinearities in driving the limit cycle behaviour. Part icular attention will be given to nonlinear interactions for subcritical LCOs. The Aero elastic Harmonic Balance formulation, allows for solutions of the coupled structural dynamics and CFD system at a reduced cost.

Shortening design time through multiplatform simulations with a portable OpenCL golden-model: the LDPC decoder case

Hardware designers and engineers typically need to explore a multi-parametric design space in order to find the best configuration for their designs using simulations that can take weeks to months to complete. For example, designers of special purpose chips need to explore parameters such as the optimal bitwidth and data representation. This is the case for the development of complex algorithms such as Low-Density Parity-Check (LDPC) decoders used in modern communication systems. Currently, high-performance computing offers a wide set of acceleration options, that range from multicore CPUs to graphics processing units (GPUs) and FPGAs. Depending on the simulation requirements, the ideal architecture to use can vary. In this paper we propose a new design flow based on OpenCL, a unified multiplatform programming model, which accelerates LDPC decoding simulations, thereby significantly reducing architectural exploration and design time. OpenCL-based parallel kernels are used without modifications or code tuning on multicore CPUs, GPUs and FPGAs. We use SOpenCL (Silicon to OpenCL), a tool that automatically converts OpenCL kernels to RTL for mapping the simulations into FPGAs. To the best of our knowledge, this is the first time that a single, unmodified OpenCL code is used to target those three different platforms. We show that, depending on the design parameters to be explored in the simulation, on the dimension and phase of the design, the GPU or the FPGA may suit different purposes more conveniently, providing different acceleration factors. For example, although simulations can typically execute more than 3x faster on FPGAs than on GPUs, the overhead of circuit synthesis often outweighs the benefits of FPGA-accelerated execution.

Multi-Dimensional Simulations of the Expanding Supernova Remnant of SN 1987A

The expanding remnant from SN 1987A is an excellent laboratory for investigating the physics of supernovae explosions. There is still a large number of outstanding questions, such as the reason for the asymmetric radio morphology, the structure of the pre-supernova environment, and the efficiency of particle acceleration at the supernova shock. We explore these questions using three-dimensional simulations of the expanding remnant between days 820 and 10,000 after the supernova. We combine a hydrodynamical simulation with semi-analytic treatments of diffusive shock acceleration and magnetic field amplification to derive radio emission as part of an inverse problem. Simulations show that an asymmetric explosion, combined with magnetic field amplification at the expanding shock, is able to replicate the persistent one-sided radio morphology of the remnant. We use an asymmetric Truelove & McKee progenitor with an envelope mass of 10 M-circle dot and an energy of 1.5 x 10(44) J. A termination shock in the progenitor's stellar wind at a distance of 0 ''.43-0 ''.51 provides a good fit to the turn on of radio emission around day 1200. For the H II region, a minimum distance of 0 ''.63 +/- 0 ''.01 and maximum particle number density of (7.11 +/- 1.78) x 10(7) m(-3) produces a good fit to the evolving average radius and velocity of the expanding shocks from day 2000 to day 7000 after explosion. The model predicts a noticeable reduction, and possibly a temporary reversal, in the asymmetric radio morphology of the remnant after day 7000, when the forward shock left the eastern lobe of the equatorial ring.

Automatic extraction of Reduced order models from CFD simulations for building energy modeling

Thermal comfort is defined as “that condition of mind which expresses satisfaction with the thermal environment’ [1] [2]. Field studies have been completed in order to establish the governing conditions for thermal comfort [3]. These studies showed that the internal climate of a room was the strongest factor in establishing thermal comfort. Direct manipulation of the internal climate is necessary to retain an acceptable level of thermal comfort. In order for Building Energy Management Systems (BEMS) strategies to be efficiently utilised it is necessary to have the ability to predict the effect that activating a heating/cooling source (radiators, windows and doors) will have on the room. The numerical modelling of the domain can be challenging due to necessity to capture temperature stratification and/or different heat sources (radiators, computers and human beings). Computational Fluid Dynamic (CFD) models are usually utilised for this function because they provide the level of details required. Although they provide the necessary level of accuracy these models tend to be highly computationally expensive especially when transient behaviour needs to be analysed. Consequently they cannot be integrated in BEMS. This paper presents and describes validation of a CFD-ROM method for real-time simulations of building thermal performance. The CFD-ROM method involves the automatic extraction and solution of reduced order models (ROMs) from validated CFD simulations. The test case used in this work is a room of the Environmental Research Institute (ERI) Building at the University College Cork (UCC). ROMs have shown that they are sufficiently accurate with a total error of less than 1% and successfully retain a satisfactory representation of the phenomena modelled. The number of zones in a ROM defines the size and complexity of that ROM. It has been observed that ROMs with a higher number of zones produce more accurate results. As each ROM has a time to solution of less than 20 seconds they can be integrated into the BEMS of a building which opens the potential to real time physics based building energy modelling.

Docking the value of pigmeat? Prevalence and financial implications of welfare lesions in Irish slaughter pigs.

Expansion of the meat inspection process to incorporate animal-based welfare measurements could contribute towards significant improvements in pig (Sus scrofa domesticus) welfare and farm profitability. This study aimed to determine the prevalence of different welfare-related lesions on the carcase and their relationship with carcase condemnations (CC) and carcase weight (CW). The financial implications of losses associated with CC and CW reductions related to the welfare lesions were also estimated. Data on tail lesions, loin bruising and bursitis, CW and condemnation/trimming outcome (and associated weights) were collected for 3,537slaughter pigs (mean [± SEM] carcase weight: 79.2 [± 8.82] kg). Overall, 72.5% of pigs had detectable tail lesions, whilst 16.0 and 44.0% were affected by severe loin bruising and hind limb bursitis, respectively. There were 2.5% of study carcases condemned and a further 3.3% were trimmed. The primary cause of CC was abscessation. While tail lesion severity did not increase the risk of abscessation, it was significantly associated with CC. Male pigs had a higher risk of tail lesions and of CC. The financial loss to producers associated with CC and trimmings was estimated at €1.10 per study pig. CW was reduced by up to 12 kg in cases of severe tail lesions. However, even mild lesions were associated with a significant reduction in CW of 1.2 kg. The value of the loss in potential CW associated with tail lesions was €0.59 per study pig. Combined with losses attributable to CC and trimmings this represented a loss of 43% of the profit margin per pig, at the time of the study, attributable to tail biting. These findings illustrate the magnitude of the impact of tail biting on pig welfare and on profitability of the pig industry. They also emphasise the potential contribution that the inclusion of welfare parameters at meat inspection could make to pig producers in informing herd health and welfare management plans.

Vlasov-kinetic computer simulations of electrostatic waves in dusty plasmas: an overview of recent results

A series of numerical simulations based on a recurrence-free Vlasov kinetic model using kinetic phase point trajectories are presented. Electron-ion plasmas and three-component (electron-ion-dust) dusty or complex plasmas are considered, via independent simulations. Considering all plasma components modeled through a kinetic approach, the linear and nonlinear behavior of ion-acoustic excitations is investigated. Maxwellian and kappa-type (superthermal) distribution functions are assumed, as initial conditions, in separate simulations for the sake of comparison. The focus is on the parametric dependence of ion-acoustic waves on the electron-to-ion temperature ratio and on the dust concentration. © 2014 EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg.

Automatic extraction of reduced-order models from CFD simulations for building energy modelling

Accurate modelling of the internal climate of buildings is essential if Building Energy Management Systems (BEMS) are to efficiently maintain adequate thermal comfort. Computational fluid dynamics (CFD) models are usually utilised to predict internal climate. Nevertheless CFD models, although providing the necessary level of accuracy, are highly computationally expensive, and cannot practically be integrated in BEMS. This paper presents and describes validation of a CFD-ROM method for real-time simulations of building thermal performance. The CFD-ROM method involves the automatic extraction and solution of reduced order models (ROMs) from validated CFD simulations. ROMs are shown to be adequately accurate with a total error below 5% and to retain satisfactory representation of the phenomena modelled. Each ROM has a time to solution under 20seconds, which opens the potential of their integration with BEMS, giving real-time physics-based building energy modelling. A parameter study was conducted to investigate the applicability of the extracted ROM to initial boundary conditions different from those from which it was extracted. The results show that the ROMs retained satisfactory total errors when the initial conditions in the room were varied by ±5°C. This allows the production of a finite number of ROMs with the ability to rapidly model many possible scenarios.

A Review of Wave Makers for 3D Numerical Simulations

Numerical methods have enabled the simulation of complex problems in off-shore and marine engineering. A significant challenge in these simulations is the creation of a realistic wave field. A good numerical tank requires wave creation and absorption of waves at various locations. Several numerical wavemakers with these capabilities have been presented in the past. This paper reviews four different wave-maker methods and discusses limitations, computational efficiency, requirements on the mesh and preprocessing and complexity of implementation.

Alfvén Waves in Simulations of Solar Photospheric Vortices

Using advanced numerical magneto-hydrodynamic simulations of the magnetized solar photosphere, including non-gray radiative transport and a non-ideal equation of state, we analyze plasma motions in photospheric magnetic vortices. We demonstrate that apparent vortex-like motions in photospheric magnetic field concentrations do not exhibit "tornado"-like behavior or a "bath-tub" effect. While at each time instance the velocity field lines in the upper layers of the solar photosphere show swirls, the test particles moving with the time-dependent velocity field do not demonstrate such structures. Instead, they move in a wave-like fashion with rapidly changing and oscillating velocity field, determined mainly by magnetic tension in the magnetized intergranular downflows. Using time-distance diagrams, we identify horizontal motions in the magnetic flux tubes as torsional Alfvén perturbations propagating along the nearly vertical magnetic field lines with local Alfvén speed.