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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

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Scalable Molecular Dynamics with NAMD

http://kth.diva-portal.org/smash/get/diva2:1303357/FULLTEXT01

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

: Presentation Outline: Review of project objective and plan; Refresher on service discovery protocols; Outline of technical approach to understand fault-tolerant behavior of service discover protocols; Initial results comparing behavior of Jini and universal plug-and-play (UPnP) when propagating information during interface failure; Plan for next six months; Conclusions.

Self-Adaptive Discovery Mechanisms for Improved Performance in Fault-Tolerant Networks

Summary form only given, as follows. A 2D electromagnetic PIC-MCC simulation of a large area plasma source is being performed. In this simulation, the plasma is contained in a metal bound cylindrical region. In one version, the plasma is excited by a ring slot on top of the chamber by oscillatory radial electric fields across the slot. The simulation demonstrates the initiation and fill-in process of a slot excited surface wave sustained plasma source. The steady state density is compared with the predictions of a simple model of the diffusion of the plasma from the source. In the diffusion model, plasma undergoes ambipolar diffusion and is only lost at the walls. Also, the role of electromagnetic effects, such as ponderomotive forces, in the initiation and fill-in are explored.

2D electromagnetic PIC-MCC simulation of the initiation of a large area surface wave sustained plasma source

To support the design and analysis of x-ray radiographic facilities and experiments at Los Alamos, we have developed an integrated chain model, which is a set of linked physics simulation codes to generate self-consistent synthetic radiographs of experiments [1]. The expectation-maximization (EM) algorithm [2] has recently been used to great advantage to link particle- in-cell (PIC) methods, which model electron propagation to a converter target, and Monte Carlo transport methods, which model bremsstrahlung photon generation and transport through the radiographic object onto a detector. The EM algorithm is a maximum- likelihood technique to estimate the probability density function (PDF) of a set of measurements. A high performance implementation of the EM algorithm to characterize multidimensional data sets using a PDF parameterized as a Gaussian mixture has been developed (GMIX). The resulting PDFs compare favorably to histograms / tallies---no binning artifacts and less noisy (especially in the tails). GMIX is being used extensively in the radiographic chain model to quantify bremsstrahlung x-ray emission from rod-pinch diodes and other devices. In particular, the PIC simulation code MERLIN is used to model the dynamics of the rod-pinch diode in the Los Alamos radiographic machine Cygnus for the linked calculations. The rod-pinch diode used in Cygnus consists of a 9- mm diameter aperture cathode and a 0.75- mm diameter needle anode. A TEM pulse launched at one simulation boundary sets up the voltage required for the electron emission. The electron trajectories are followed self-consistently in the electromagnetic fields as the electron beam pinches at the anode tip with energies up to 2.25 MeV. The Monte Carlo transport code MCNP is used to track the bremsstrahlung photons generated by electrons incident on the anode tip. GMIX is used to “upsample” the PIC electrons to provide a suitably large population for the Monte Carlo calculation (10 7 or greater) that would have been computationally expensive to generate directly. The motivation, the mathematical properties, and the implementation details, and applications of GMIX to plasma and Monte Carlo simulations will be discussed, including: improved coupling of PIC to Monte Carlo simulations, adaptive PIC simulations, and characterization of the Cygnus radiographic parameters such as energy and angular spectra, spot size, and dose.

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A Maximum Likelihood Method for Linking of Particle-in-Cell and Monte Carlo Simulations

Fully electromagnetic particle-in-cell simulations of tearing modes in two-dimensional plane geometry in a force-free reversed field pinch (RFP)-like plasma equilibrium are performed to study possible kinetic effects on these modes in RFPs Linear tearing modes are compared in the kinetic and two fluid models The results showed that the growth rates and the profiles of magnetic field components in the two models are very similar, indicating that the kinetic effects on the studied tearing modes are weak such that the two fluid approximation is rather accurate for modeling these instabilities in RFPs During the nonlinear evolution of the tearing mode in this geometry, small scale secondary instabilities located near the internal layer of the primary tearing instability are excited These secondary instabilities appear to be driven by the nonlinearly induced local pressure gradient in the regions of unfavorable curvature of the nonlinearly evolved magnetic field They could also appear in a realistic RFP g

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Kevin J. Bowers

Papers

Self-Adaptive Discovery Mechanisms for Improved Performance in Fault-Tolerant Networks

2D electromagnetic PIC-MCC simulation of the initiation of a large area surface wave sustained plasma source

A Maximum Likelihood Method for Linking of Particle-in-Cell and Monte Carlo Simulations

Particle-in-cell simulations of tearing modes in reversed-field-pinch-like plasma

Skalierbares Verfahren zur Berechnung von entfernungsbeschränkten paarweisen Teilchenwechselwirkungen