Related papers: Efficient molecular dynamics simulations with many…

A finite-difference Micromagnetic simulation code written in MATLAB is presented with Graphics Processing Unit (GPU) acceleration. The high performance of Graphics Processing Unit (GPU) is demonstrated compared to a typical Central…

While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular…

We present a way to combine Vlasov and two-fluid codes for the simulation of a collisionless plasma in large domains while keeping full information of the velocity distribution in localized areas of interest. This is made possible by…

In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated…

Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…

Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…

As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…

Graphics Processing Units (GPUs) have become the standard in accelerating scientific applications on heterogeneous systems. However, as GPUs are getting faster, one potential performance bottleneck with GPU-accelerated applications is the…

Memcomputing is a novel paradigm of computation that utilizes dynamical elements with memory to both store and process information on the same physical location. Its building blocks can be fabricated in hardware with standard electronic…

Graphics Processing Units (GPUs) are being used in many areas of physics, since the performance versus cost is very attractive. The GPUs can be addressed by CUDA which is a NVIDIA's parallel computing architecture. It enables dramatic…

In this paper we describe and demonstrate a C++ code written to determine the trajectory of particles traversing oriented single crystals and a CUDA code written to evaluate the radiation spectra from charged particles with arbitrary…

We present the GPU version of DeePMD-kit, which, upon training a deep neural network model using ab initio data, can drive extremely large-scale molecular dynamics (MD) simulation with ab initio accuracy. Our tests show that the GPU version…

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…

Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…

Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale…

We examine the problem of optimizing classification tree evaluation for on-line and real-time applications by using GPUs. Looking at trees with continuous attributes often used in image segmentation, we first put the existing algorithms for…

This paper investigates the application of a robust CPU-based power modelling methodology that performs an automatic search of explanatory events derived from performance counters to embedded GPUs. A 64-bit Tegra TX1 SoC is configured with…

This paper satisfies the reproducibility challenge of the Student Cluster Competition at Supercomputing 2017. We attempted to reproduce the results of H\"{o}hnerbach et al. (2016) for an implementation of a vectorized code for the Tersoff…

Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…

The NVIDIA Volta GPU microarchitecture introduces a specialized unit, called "Tensor Core" that performs one matrix-multiply-and-accumulate on 4x4 matrices per clock cycle. The NVIDIA Tesla V100 accelerator, featuring the Volta…