ILU Smoothers for AMG with Scaled Triangular Factors

ILU smoothers are effective in the algebraic multigrid (AMG) V-cycle for reducing high-frequency components of the residual error. However, direct triangular solves are comparatively slow on GPUs. Previous work by Chow and Patel (2015) and Antz et al. (2015) demonstrated the advantages of Jacobi relaxation as an alternative. Depending on the threshold and fill-level parameters chosen, the factors are highly non-normal and Jacobi is unlikely to converge in a low number of iterations. The Ruiz algorithm applies row or row/column scaling to U in order to reduce the departure from normality. The inherently sequential solve is replaced with a Richardson iteration. There are several advantages beyond the lower compute time. Scaling is performed locally for a diagonal block of the global matrix because it is applied directly to the factor. An ILUT Schur complement smoother maintains a constant GMRES iteration count as the number of MPI ranks increases and thus parallel strong-scaling is improved. The new algorithms are included in hypre, and achieve improved time to solution for several Exascale applications, including the Nalu-Wind and PeleLM pressure solvers. For large problem sizes, GMRES+AMG with iterative triangular solves execute at least five times faster than with direct on massively-parallel GPUs.Comment: v2 updated citation information; v3 updated results; v4 abstract updated, new results added; v5 new experimental analysis and results adde

Chaotic Advection and the Emergence of Tori in the K\"uppers-Lortz State

Motivated by the roll-switching behavior observed in rotating Rayleigh-B\'enard convection, we define a K\"uppers-Lortz (K-L) state as a volume-preserving flow with periodic roll switching. For an individual roll state, the Lagrangian particle trajectories are periodic. In a system with roll-switching, the particles can exhibit three-dimensional, chaotic motion. We study a simple phenomenological map that models the Lagrangian dynamics in a K-L state. When the roll axes differ by $120^{\circ}$ in the plane of rotation, we show that the phase space is dominated by invariant tori if the ratio of switching time to roll turnover time is small. When this parameter approaches zero these tori limit onto the classical hexagonal convection patterns, and, as it gets large, the dynamics becomes fully chaotic and well-mixed. For intermediate values, there are interlinked toroidal and poloidal structures separated by chaotic regions. We also compute the exit time distributions and show that the unbounded chaotic orbits are normally diffusive. Although the map presumes instantaneous switching between roll states, we show that the qualitative features of the flow persist when the model has smooth, overlapping time-dependence for the roll amplitudes (the Busse-Heikes model).Comment: laTeX, 23 pages, 7 figure

Laser-Plasma Wakefield Acceleration with Higher Order Laser Modes

Laser-plasma collider designs point to staging of multiple accelerator stages at the 10 GeV level, which are to be developed on the upcoming BELLA laser, while Thomson Gamma source designs use GeV stages, both requiring efficiency and low emittance. Design and scaling of stages operating in the quasi-linear regime to address these needs are presented using simulations in the VORPAL framework. In addition to allowing symmetric acceleration of electrons and positrons, which is important for colliders, this regime has the property that the plasma wakefield is proportional to the transverse gradient of the laser intensity profile. We demonstrate use of higher order laser modes to tailor the laser pulse and hence the transverse focusing forces in the plasma. In particular, we show that by using higher order laser modes, we can reduce the focusing fields and hence increase the matched electron beam radius, which is important to increased charge and efficiency, while keeping the low bunch emittance required for applications

Bayesian estimation of prevalence of paratuberculosis in dairy herds enrolled in a voluntary Johne’s Disease Control Programme in Ireland

Bovine paratuberculosis is a disease characterised by chronic granulomatous enteritis which manifests clinically as a protein-losing enteropathy causing diarrhoea, hypoproteinaemia, emaciation and, eventually death. Some evidence exists to suggest a possible zoonotic link and a national voluntary Johne’s Disease Control Programme was initiated by Animal Health Ireland in 2013. The objective of this study was to estimate herd-level true prevalence (HTP) and animal-level true prevalence (ATP) of paratuberculosis in Irish herds enrolled in the national voluntary JD control programme during 2013–14. Two datasets were used in this study. The first dataset had been collected in Ireland during 2005 (5822 animals from 119 herds), and was used to construct model priors. Model priors were updated with a primary (2013–14) dataset which included test records from 99,101 animals in 1039 dairy herds and was generated as part of the national voluntary JD control programme. The posterior estimate of HTP from the final Bayesian model was 0.23–0.34 with a 95% probability. Across all herds, the median ATP was found to be 0.032 (0.009, 0.145). This study represents the first use of Bayesian methodology to estimate the prevalence of paratuberculosis in Irish dairy herds. The HTP estimate was higher than previous Irish estimates but still lower than estimates from other major dairy producing countries

Computational studies and optimization of wakefield accelerators

Laser- and particle beam-driven plasma wakefield accelerators produce accelerating fields thousands of times higher than radio-frequency accelerators, offering compactness and ultrafast bunches to extend the frontiers of high energy physics and to enable laboratory-scale radiation sources. Large-scale kinetic simulations provide essential understanding of accelerator physics to advance beam performance and stability and show and predict the physics behind recent demonstration of narrow energy spread bunches. Benchmarking between codes is establishing validity of the models used and, by testing new reduced models, is extending the reach of simulations to cover upcoming meter-scale multi-GeV experiments. This includes new models that exploit Lorentz boosted simulation frames to speed calculations. Simulations of experiments showed that recently demonstrated plasma gradient injection of electrons can be used as an injector to increase beam quality by orders of magnitude. Simulations are now also modeling accelerator stages of tens of GeV, staging of modules, and new positron sources to design next-generation experiments and to use in applications in high energy physics and light sources

A community resource for paired genomic and metabolomic data mining

Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.Peer reviewe

COMPASS, the COMmunity Petascale project for Accelerator Science and Simulation, a board computational accelerator physics initiative

Accelerators are the largest and most costly scientific instruments of the Department of Energy, with uses across a broad range of science, including colliders for particle physics and nuclear science and light sources and neutron sources for materials studies. COMPASS, the Community Petascale Project for Accelerator Science and Simulation, is a broad, four-office (HEP, NP, BES, ASCR) effort to develop computational tools for the prediction and performance enhancement of accelerators. The tools being developed can be used to predict the dynamics of beams in the presence of optical elements and space charge forces, the calculation of electromagnetic modes and wake fields of cavities, the cooling induced by comoving beams, and the acceleration of beams by intense fields in plasmas generated by beams or lasers. In SciDAC-1, the computational tools had multiple successes in predicting the dynamics of beams and beam generation. In SciDAC-2 these tools will be petascale enabled to allow the inclusion of an unprecedented level of physics for detailed prediction

Resonances in compound processes

The first-exit time of a compound process with strictly positive jumps reaching a horizontal barrier is considered. The first-exit time distribution for the specific case of Poisson arrivals and gamma distributed jump sizes is derived. If the jump size distribution converges weakly to a Dirac delta function as the variance tends to zero, the process tends to a compound process with constant jump size. In the case when the barrier is an exact multiple of the constant jump size a small peculiarity arises; the firstexit time distribution with general jumps does not tend to the first-exit time distribution with constant jumps. The first-exit time distribution for M/G/1 queues with gamma distributed service times is shown to have the same peculiarity