Related papers: Efficient molecular dynamics simulations with many…
Growing deployment of power and energy efficient throughput accelerators (GPU) in data centers demands enhancement of power-performance co-optimization capabilities of GPUs. Realization of exascale computing using accelerators requires…
This paper presents two conceptually simple methods for parallelizing a Parallel Tempering Monte Carlo simulation in a distributed volunteer computing context, where computers belonging to the general public are used. The first method uses…
We present and discuss the characteristics and performances, both in term of computational speed and precision, of a numerical code which numerically integrates the equation of motions of N 'particles' interacting via Newtonian gravitation…
This article presents an optimized algorithm and implementation for calculating resolution-of-the-identity Hartree-Fock (RI-HF) energies and analytic gradients using multiple Graphics Processing Units (GPUs). The algorithm is especially…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
We present an implementation of all-electron density-functional theory for massively parallel GPGPU-based platforms, using localized atom-centered basis functions and real-space integration grids. Special attention is paid to domain…
Computational Fluid Dynamics (CFD) is the simulation of fluid flow undertaken with the use of computational hardware. The underlying equations are computationally challenging to solve and necessitate high performance computing (HPC) to…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
We accelerated an ab-initio molecular QMC calculation by using GPGPU. Only the bottle-neck part of the calculation is replaced by CUDA subroutine and performed on GPU. The performance on a (single core CPU + GPU) is compared with that on a…
One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…
We report the first CUDA graphics-processing-unit (GPU) implementation of the polymer field-theoretic simulation framework for determining fully fluctuating expectation values of equilibrium properties for periodic and select aperiodic…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
We propose a hybrid tree algorithm for reducing calculation and communication cost of collision-less N-body simulations. The concept of our algorithm is that we split interaction force into two parts: hard-force from neighbor particles and…
A modern graphics processing unit (GPU) is able to perform massively parallel scientific computations at low cost. We extend our implementation of the checkerboard algorithm for the two dimensional Ising model [T. Preis et al., J. Comp.…
We review the recent optimizations of gravitational $N$-body kernels for running them on graphics processing units (GPUs), on single hosts and massive parallel platforms. For each of the two main $N$-body techniques, direct summation and…
Computing on graphics processors is maybe one of the most important developments in computational science to happen in decades. Not since the arrival of the Beowulf cluster, which combined open source software with commodity hardware to…
Magnetohydrodynamic (MHD) simulations based on the ideal MHD equations have become a powerful tool for modeling phenomena in a wide range of applications including laboratory, astrophysical, and space plasmas. In general, high-resolution…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…