Related papers: Efficient Parallel Algorithm for Statistical Ion T…
The Particle-In-Cell (PIC) method for plasma simulation tracks particle phase space information using particle and grid data structures. High computational costs in 2D and 3D device-scale PIC simulations necessitate parallelization, with…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have…
Quantum-based molecular dynamics (QMD) is a highly accurate and transferable method for material science simulations. However, the time scales and system sizes accessible to QMD are typically limited to picoseconds and a few hundred atoms.…
For the last thirty years, several Dynamic Memory Managers (DMMs) have been proposed. Such DMMs include first fit, best fit, segregated fit and buddy systems. Since the performance, memory usage and energy consumption of each DMM differs,…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
We investigate the parallel performance of Parallel Spectral Deferred corrections, a numerical approach that provides small-scale parallelism for the numerical solution of initial value problems. The scheme is applied to the shallow-water…
We provide a mathematically proven parallelization scheme for particle methods on distributed-memory computer systems. Particle methods are a versatile and widely used class of algorithms for computer simulations and numerical predictions…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
Compton cameras are radiation detectors that provide spatial information on the origin of the {\gamma}-ray sources based on the Compton scattering effect. Many applications require these detectors to be used at high counting rate. As such,…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
We experiment with a massively parallel implementation of an algorithm for simulating the dynamics of metastable decay in kinetic Ising models. The parallel scheme is directly applicable to a wide range of stochastic cellular automata where…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
In this study, we have developed a parallel version of the random time simulation algorithm. Firstly, we gave a rigorous basis of the random time description of the stochastic process of chemical reaction network time evolution. And then we…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
We introduce efficient parallel algorithms for sampling from the Gibbs distribution and estimating the partition function of Ising models. These algorithms achieve parallel efficiency, with polylogarithmic depth and polynomial total work,…
Decoupling approach presents a novel solution/alternative to the highly time-consuming fluid-thermal-structural simulation procedures when thermal effects and resultant displacements on machine tools are analyzed. Using high dimensional…
We present a new numerical scheme to solve the transfer of diffuse radiation on three-dimensional mesh grids which is efficient on processors with highly parallel architecture such as recently popular GPUs and CPUs with multi- and many-core…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…