Accurate modeling of parallel scientific computations

Scientific codes are usually parallelized by partitioning a grid among processors. To achieve top performance it is necessary to partition the grid so as to balance workload and minimize communication/synchronization costs. This problem is particularly acute when the grid is irregular, changes over the course of the computation, and is not known until load time. Critical mapping and remapping decisions rest on the ability to accurately predict performance, given a description of a grid and its partition. This paper discusses one approach to this problem, and illustrates its use on a one-dimensional fluids code. The models constructed are shown to be accurate, and are used to find optimal remapping schedules

Secondary frequencies in the wake of a circular cylinder with vortex shedding

A detailed numerical study of two-dimensional flow past a circular cylinder at moderately low Reynolds numbers was conducted using three different numerical algorithms for solving the time-dependent compressible Navier-Stokes equations. It was found that if the algorithm and associated boundary conditions were consistent and stable, then the major features of the unsteady wake were well-predicted. However, it was also found that even stable and consistent boundary conditions could introduce additional periodic phenomena reminiscent of the type seen in previous wind-tunnel experiments. However, these additional frequencies were eliminated by formulating the boundary conditions in terms of the characteristic variables. An analysis based on a simplified model provides an explanation for this behavior

Direct thermal desorption gas chromatographic determination of toxicologically relevant concentrations of ethylene glycol in whole blood

© 2018 The Royal Society of Chemistry. A simple and rapid method involving thermal desorption gas chromatography (TD-GC) with flame ionisation detection has been successfully developed for the determination of ethylene glycol in whole blood. No sample extraction or derivatization steps were required. The conditions required for the direct determination of ethylene glycol in whole blood were optimised and require only the addition of the internal standard, 1,2-butanediol, to the sample. A 1 μL aliquot of the sample was then introduced to the thermal desorption unit, dried, and thermally desorbed directly to the gas chromatograph. A calibration curve was constructed over the concentration range of 1.0 to 200 mM and was found to be linear over the range investigated with an R2 value of 0.9997. The theoretical limit of detection based on 3σ was calculated to be 50.2 μM (3.11 mg L-1). No issues with carryover were recorded. No interferences were recorded from endogenous blood components or a number of commonly occurring alcohols. The proposed method was evaluated by carrying out replicate ethylene glycol determinations on fortified whole blood samples at the levels of 12.5 mM, 20.0 mM, 31.2 mM, 100 mM and 200 mM comparable to commonly reported blood levels in intoxications. Mean recoveries of between 84.8% and 107% were obtained with coefficients of variation of between 1.7% and 5.8%. These data suggest that the method holds promise for applications in toxicology, where a rapid, reliable method to confirm ethylene glycol poisoning is required

Time Averaged Quantum Dynamics and the Validity of the Effective Hamiltonian Model

We develop a technique for finding the dynamical evolution in time of an averaged density matrix. The result is an equation of evolution that includes an Effective Hamiltonian, as well as decoherence terms in Lindblad form. Applying the general equation to harmonic Hamiltonians, we confirm a previous formula for the Effective Hamiltonian together with a new decoherence term which should in general be included, and whose vanishing provides the criteria for validity of the Effective Hamiltonian approach. Finally, we apply the theory to examples of the AC Stark Shift and Three- Level Raman Transitions, recovering a new decoherence effect in the latter.Comment: 7 pages, 2 figure

A semantic Grid for molecular science

Proceedings of the 2003 UK e-Science All Hands Meeting, 31st August - 3rd September, Nottingham UKThe properties of molecules have very well defined semantics and allow the creation of a semantic GRID. Markup languages (CML - Chemical Markup Language) and dictionary-based ontologies have been designed to support a wide range of applications, including chemical supply, publication and the safety of compounds. Many properties can be computed by Quantum Mechanical (QM) programs and we have developed a "black-box" system based on XML wrappers for all components. This is installed on a Condor system on which we have computed properties for 250, 000 compounds. The results of this will be available in an OpenData/OpenSource peer-to-peer (P2P) system (WorldWide Molecular Matrix - WWMM)

A programming environment for distributed complex computing. An overview of the Framework for Interdisciplinary Design Optimization (FIDO) project. NASA Langley TOPS exhibit H120b

The Framework for Interdisciplinary Design Optimization (FIDO) is a general programming environment for automating the distribution of complex computing tasks over a networked system of heterogeneous computers. For example, instead of manually passing a complex design problem between its diverse specialty disciplines, the FIDO system provides for automatic interactions between the discipline tasks and facilitates their communications. The FIDO system networks all the computers involved into a distributed heterogeneous computing system, so they have access to centralized data and can work on their parts of the total computation simultaneously in parallel whenever possible. Thus, each computational task can be done by the most appropriate computer. Results can be viewed as they are produced and variables changed manually for steering the process. The software is modular in order to ease migration to new problems: different codes can be substituted for each of the current code modules with little or no effect on the others. The potential for commercial use of FIDO rests in the capability it provides for automatically coordinating diverse computations on a networked system of workstations and computers. For example, FIDO could provide the coordination required for the design of vehicles or electronics or for modeling complex systems

Multi-Element Regulation of the Tropical Forest Carbon Cycle

Tropical ecosystems dominate the exchange of carbon dioxide between the atmosphere and terrestrial biosphere, yet our understanding of how nutrients control the tropical carbon (C) cycle remains far from complete. In part, this knowledge gap arises from the marked complexity of the tropical forest biome, in which nitrogen, phosphorus, and perhaps several other elements may play roles in determining rates of C gain and loss. As studies from other ecosystems show, failing to account for nutrient–C interactions can lead to substantial errors in predicting how ecosystems will respond to climate and other environmental changes. Thus, although resolving the complex nature of tropical forest nutrient limitation – and then incorporating such knowledge into predictive models – will be difficult, it is a challenge that the global change community must address

Twin Studies: Research in Genes, Teeth and Faces

This volume is about an ongoing long-term research initiative led by researchers from the School of Dentistry at the University of Adelaide. The aim of this book is to provide an overview of the studies of the teeth and faces of Australian twins and their families that have extended over more than thirty years

Optimization of switching losses and capacitor voltage ripple using model predictive control of a cascaded H-bridge multi-level StatCom

This paper further develops a Model Predictive Control (MPC) scheme which is able to exploit the large number of redundant switching states available in a multi-level H-bridge StatCom (H-StatCom). The new sections of the scheme provide optimised methods to trade off the harmonic performance with converter switching losses and capacitor voltage ripple. Varying the pulse placement within the modulation scheme and modifying the heuristic model of the voltage balancing characteristics allows the MPC scheme to achieve superior performance to that of the industry standard phase shifted carrier modulation technique. The effects of capacitor voltage ripple on the lifetime of the capacitors is also investigated. It is shown that the MPC scheme can reduce capacitor voltage ripple and increase capacitor lifetime. Simulation and experimental results are presented that confirm the correct operation of the control and modulation strategies