DISPATCH: A Numerical Simulation Framework for the Exa-scale Era. I. Fundamentals

We introduce a high-performance simulation framework that permits the semi-independent, task-based solution of sets of partial differential equations, typically manifesting as updates to a collection of `patches' in space-time. A hybrid MPI/OpenMP execution model is adopted, where work tasks are controlled by a rank-local `dispatcher' which selects, from a set of tasks generally much larger than the number of physical cores (or hardware threads), tasks that are ready for updating. The definition of a task can vary, for example, with some solving the equations of ideal magnetohydrodynamics (MHD), others non-ideal MHD, radiative transfer, or particle motion, and yet others applying particle-in-cell (PIC) methods. Tasks do not have to be grid-based, while tasks that are, may use either Cartesian or orthogonal curvilinear meshes. Patches may be stationary or moving. Mesh refinement can be static or dynamic. A feature of decisive importance for the overall performance of the framework is that time steps are determined and applied locally; this allows potentially large reductions in the total number of updates required in cases when the signal speed varies greatly across the computational domain, and therefore a corresponding reduction in computing time. Another feature is a load balancing algorithm that operates `locally' and aims to simultaneously minimise load and communication imbalance. The framework generally relies on already existing solvers, whose performance is augmented when run under the framework, due to more efficient cache usage, vectorisation, local time-stepping, plus near-linear and, in principle, unlimited OpenMP and MPI scaling.Comment: 17 pages, 8 figures. Accepted by MNRA

Abundance Analysis of the Halo Giant HD122563 with Three-Dimensional Model Stellar Atmospheres

We present a preliminary local thermodynamic equilibrium (LTE) abundance analysis of the template halo red giant HD122563 based on a realistic, three-dimensional (3D), time-dependent, hydrodynamical model atmosphere of the very metal-poor star. We compare the results of the 3D analysis with the abundances derived by means of a standard LTE analysis based on a classical, 1D, hydrostatic model atmosphere of the star. Due to the different upper photospheric temperature stratifications predicted by 1D and 3D models, we find large, negative, 3D-1D LTE abundance differences for low-excitation OH and Fe I lines. We also find trends with lower excitation potential in the derived Fe LTE abundances from Fe I lines, in both the 1D and 3D analyses. Such trends may be attributed to the neglected departures from LTE in the spectral line formation calculations.Comment: 4 pages, 4 figures, contribution to proceedings for Joint Discussion 10 at the IAU General Assembly, Rio de Janeiro, Brazil, August 200

A simulation of solar convection at supergranulation scale

We present here numerical simulations of surface solar convection which cover a box of 30$\times30\times$3.2 Mm$^3$ with a resolution of 315$\times315\times$82, which is used to investigate the dynamics of scales larger than granulation. No structure resembling supergranulation is present; possibly higher Reynolds numbers (i.e. higher numerical resolution), or magnetic fields, or greater depth are necessary. The results also show interesting aspects of granular dynamics which are briefly presented, like extensive p-mode ridges in the k-$\omega$ diagram and a ringlike distribution of horizontal vorticity around granules. At large scales, the horizontal velocity is much larger than the vertical velocity and the vertical motion is dominated by p-mode oscillations.Comment: Contribution to the proceedings of the workshop entitled "THEMIS and the new frontiers of solar atmosphere dynamics" (March 2001), 6 pages, to appear in Nuovo Cimento

Numerical constraints on the model of stochastic excitation of solar-type oscillations

Analyses of a 3D simulation of the upper layers of a solar convective envelope provide constraints on the physical quantities which enter the theoretical formulation of a stochastic excitation model of solar p modes, for instance the convective velocities and the turbulent kinetic energy spectrum. These constraints are then used to compute the acoustic excitation rate for solar p modes, P. The resulting values are found ~5 times larger than the values resulting from a computation in which convective velocities and entropy fluctuations are obtained with a 1D solar envelope model built with the time-dependent, nonlocal Gough (1977) extension of the mixing length formulation for convection (GMLT). This difference is mainly due to the assumed mean anisotropy properties of the velocity field in the excitation region. The 3D simulation suggests much larger horizontal velocities compared to vertical ones than in the 1D GMLT solar model. The values of P obtained with the 3D simulation constraints however are still too small compared with the values inferred from solar observations. Improvements in the description of the turbulent kinetic energy spectrum and its depth dependence yield further increased theoretical values of P which bring them closer to the observations. It is also found that the source of excitation arising from the advection of the turbulent fluctuations of entropy by the turbulent movements contributes ~ 65-75 % to the excitation and therefore remains dominant over the Reynolds stress contribution. The derived theoretical values of P obtained with the 3D simulation constraints remain smaller by a factor ~3 compared with the solar observations. This shows that the stochastic excitation model still needs to be improved.Comment: 11 pages, 9 figures, accepted for publication in A&

Effects of different vibration frequencies, amplitudes and contraction levels on lower limb muscles during graded isometric contractions superimposed on whole body vibration stimulation

Background: Indirect vibration stimulation, i.e., whole body vibration or upper limb vibration, has been investigated increasingly as an exercise intervention for rehabilitation applications. However, there is a lack of evidence regarding the effects of graded isometric contractions superimposed on whole body vibration stimulation. Hence, the objective of this study was to quantify and analyse the effects of variations in the vibration parameters and contraction levels on the neuromuscular responses to isometric exercise superimposed on whole body vibration stimulation. Methods: In this study, we assessed the 'neuromuscular effects' of graded isometric contractions, of 20%, 40%, 60%, 80% and 100% of maximum voluntary contraction, superimposed on whole body vibration stimulation (V) and control (C), i.e., no-vibration in 12 healthy volunteers. Vibration stimuli tested were 30 Hz and 50 Hz frequencies and 0.5 mm and 1.5 mm amplitude. Surface electromyographic activity of the vastus lateralis, vastus medialis and biceps femoris were measured during V and C conditions with electromyographic root mean square and electromyographic mean frequency values used to quantify muscle activity and their fatigue levels, respectively. Results: Both the prime mover (vastus lateralis) and the antagonist (biceps femoris) displayed significantly higher (P < 0.05) electromyographic activity with the V than the C condition with varying percentage increases in EMG root-mean-square (EMGrms) values ranging from 20% to 200%. For both the vastus lateralis and biceps femoris, the increase in mean EMGrms values depended on the frequency, amplitude and muscle contraction level with 50 Hz-0.5 mm stimulation inducing the largest neuromuscular activity. Conclusions: These results show that the isometric contraction superimposed on vibration stimulation leads to higher neuromuscular activity compared to isometric contraction alone in the lower limbs. The combination of the vibration frequency with the amplitude and the muscle tension together grades the final neuromuscular output.Peer reviewe

Solar Oscillations and Convection: II. Excitation of Radial Oscillations

Solar p-mode oscillations are excited by the work of stochastic, non-adiabatic, pressure fluctuations on the compressive modes. We evaluate the expression for the radial mode excitation rate derived by Nordlund and Stein (Paper I) using numerical simulations of near surface solar convection. We first apply this expression to the three radial modes of the simulation and obtain good agreement between the predicted excitation rate and the actual mode damping rates as determined from their energies and the widths of their resolved spectral profiles. We then apply this expression for the mode excitation rate to the solar modes and obtain excellent agreement with the low l damping rates determined from GOLF data. Excitation occurs close to the surface, mainly in the intergranular lanes and near the boundaries of granules (where turbulence and radiative cooling are large). The non-adiabatic pressure fluctuations near the surface are produced by small instantaneous local imbalances between the divergence of the radiative and convective fluxes near the solar surface. Below the surface, the non-adiabatic pressure fluctuations are produced primarily by turbulent pressure fluctuations (Reynolds stresses). The frequency dependence of the mode excitation is due to effects of the mode structure and the pressure fluctuation spectrum. Excitation is small at low frequencies due to mode properties -- the mode compression decreases and the mode mass increases at low frequency. Excitation is small at high frequencies due to the pressure fluctuation spectrum -- pressure fluctuations become small at high frequencies because they are due to convection which is a long time scale phenomena compared to the dominant p-mode periods.Comment: Accepted for publication in ApJ (scheduled for Dec 10, 2000 issue). 17 pages, 27 figures, some with reduced resolution -- high resolution versions available at http://www.astro.ku.dk/~aake/astro-ph/0008048