Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

The standard model of particle physics predicts two phase transitions that are relevant for the evolution of the early Universe. One, the quantum chromodynamics transition, involves the strong force that binds quarks into protons and neutrons. Despite much theoretical effort, the nature of this transition remains ambiguous. Now Aoki et al. report computationally demanding calculations that suggest that there was no true phase transition. Instead, an analytic crossover took place, involving a rapid, continuous change with temperature as opposed to a jump. This means that it will be difficult to find experimental evidence of a transition from astronomical observations. The standard model of particle physics predicts two transitions that are relevant for the evolution of the early Universe. Computationally demanding calculations now reveal that a real phase transition did not occur, but rather an analytic crossover, involving a rapid change (as opposed to a jump) as the temperature varies. Quantum chromodynamics (QCD) is the theory of the strong interaction, explaining (for example) the binding of three almost massless quarks into a much heavier proton or neutron—and thus most of the mass of the visible Universe. The standard model of particle physics predicts a QCD-related transition that is relevant for the evolution of the early Universe. At low temperatures, the dominant degrees of freedom are colourless bound states of hadrons (such as protons and pions). However, QCD is asymptotically free, meaning that at high energies or temperatures the interaction gets weaker and weaker1,2, causing hadrons to break up. This behaviour underlies the predicted cosmological transition between the low-temperature hadronic phase and a high-temperature quark–gluon plasma phase (for simplicity, we use the word ‘phase’ to characterize regions with different dominant degrees of freedom). Despite enormous theoretical effort, the nature of this finite-temperature QCD transition (that is, first-order, second-order or analytic crossover) remains ambiguous. Here we determine the nature of the QCD transition using computationally demanding lattice calculations for physical quark masses. Susceptibilities are extrapolated to vanishing lattice spacing for three physical volumes, the smallest and largest of which differ by a factor of five. This ensures that a true transition should result in a dramatic increase of the susceptibilities. No such behaviour is observed: our finite-size scaling analysis shows that the finite-temperature QCD transition in the hot early Universe was not a real phase transition, but an analytic crossover (involving a rapid change, as opposed to a jump, as the temperature varied). As such, it will be difficult to find experimental evidence of this transition from astronomical observations.

https://arxiv.org/pdf/hep-lat/0611014.pdf

The order of the quantum chromodynamics transition predicted by the standard model of particle physics

The authors review the theory and phenomenology of instantons in quantum chromodynamics (QCD). After a general overview, they provide a pedagogical introduction to semiclassical methods in quantum mechanics and field theory. The main part of the review summarizes our understanding of the instanton liquid in QCD and the role of instantons in generating the spectrum of light hadrons. The authors also discuss properties of instantons at finite temperature and how instantons can provide a mechanism for the chiral phase transition. They give an overview of the role of instantons in some other models, in particular low-dimensional sigma models, electroweak theory, and supersymmetric QCD.

http://wonka.physics.ncsu.edu/~tmschaef/physics/RevModPhys_Instantons.pdf

Instantons in QCD

Thermodynamics of SU(3) lattice gauge theory

Dishevelled: The hub of Wnt signaling.

A hosted service provider for the Internet is operated so as to provide dynamic management of hosted services across disparate customer accounts and/or geographically distinct sites.

Method and system for providing dynamic hosted service management across disparate accounts/sites

A system for distributing incoming client requests across multiple servers in a networked client-server computer environment processes all requests as a set that occur within a given time interval and collects information on the attributes of the requests and the resource capability of the servers to dynamically allocate requests in a set to the appropriate servers upon completion of the time interval. Preferably, a request table collects at least two requests incoming within a predetermined time interval, a request examiner routine analyzes each collected request with respect to at least one attribute, a system status monitor collects resource capability information of each server in a resource table and an optimization and allocation process distributes collected requests in the request table across the multiple servers upon completion of said time interval based on an optimization of potential pairings of the requests in the request table with servers in the resource table.

System for balance distribution of requests across multiple servers using dynamic metrics

Monte Carlo calculations on lattices with large spatial volume show that the SU(3) deconfining phase transition is more weakly first order than previously thought. We have studied the transition for ${N}_{T}=4 \mathrm{and} 6$ on lattices of spatial volumes ${16}^{3}$, ${20}^{3}$, and ${24}^{3}$. The ${24}^{3}$\ifmmode\times\else\texttimes\fi{}4 calculations show a sharp first-order phase transition, yielding a latent heat $\frac{\ensuremath{\Delta}\mathcal{E}}{{T}^{4}}$ of 2.54\ifmmode\pm\else\textpm\fi{}0.12. The ${24}^{3}$\ifmmode\times\else\texttimes\fi{}6 calculations suffer greater finite-volume smearing, but suggest that $\frac{\ensuremath{\Delta}\mathcal{E}}{{T}^{4}}=2.48\ifmmode\pm\else\textpm\fi{}0.24$. Correlation lengths increase significantly near the transition, and the energy plus pressure of the ordered phase depends strongly on $\ensuremath{\beta}$.

Nature of the deconfining phase transition in SU(3) lattice gauge theory.

Parallel Simulated Annealing by Mixing of States

The book provides a practical guide to computational scientists and engineers to help advance their research by exploiting the superpower of supercomputers with many processors and complex networks. This book focuses on the design and analysis of basic parallel algorithms, the key components for composing larger packages for a wide range of applications.

Yuefan Deng

Papers

Method and system for providing dynamic hosted service management across disparate accounts/sites

System for balance distribution of requests across multiple servers using dynamic metrics

Nature of the deconfining phase transition in SU(3) lattice gauge theory.

Parallel Simulated Annealing by Mixing of States

Applied Parallel Computing