Related papers: General-purpose molecular dynamics simulations on …
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
Polymerization of C60 molecular crystal under high pressure and high temperature is simulated by using linear scaling tight binding molecular dynamics (TBMD) with Graphic Processing Unit (GPU) as a computational accelerator for…
A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, together with extensions to more complex systems. New measurements include the…
Restricted solid on solid surface growth models can be mapped onto binary lattice gases. We show that efficient simulation algorithms can be realized on GPUs either by CUDA or by OpenCL programming. We consider a deposition/evaporation…
Linear Programs (LPs) appear in a large number of applications and offloading them to the GPU is viable to gain performance. Existing work on offloading and solving an LP on GPU suggests that performance is gained from large sized LPs…
Machine learning potentials (MLPs) have advanced rapidly and show great promise to transform molecular dynamics (MD) simulations. However, most existing software tools are tied to specific MLP architectures, lack integration with standard…
We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate…
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…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
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…
The main objective of this work consists in analyzing sub-structuring method for the parallel solution of sparse linear systems with matrices arising from the discretization of partial differential equations such as finite element, finite…
We describe GPU implementations of the matrix recommender algorithms CCD++ and ALS. We compare the processing time and predictive ability of the GPU implementations with existing multi-core versions of the same algorithms. Results on the…
Due to their highly parallel multi-cores architecture, GPUs are being increasingly used in a wide range of computationally intensive applications. Compared to CPUs, GPUs can achieve higher performances at accelerating the programs'…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
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…
High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
To effectively control large-scale distributed systems online, model predictive control (MPC) has to swiftly solve the underlying high-dimensional optimization. There are multiple techniques applied to accelerate the solving process in the…
This paper focuses on the parallel implementation of a direct $N$-body method~(particle-particle algorithm) and the application of multiple GPUs for galactic dynamics simulations. Application of a hybrid OpenMP-CUDA technology is considered…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…