Related papers: Efficient Implementations of Molecular Dynamics Si…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…
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…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…
This paper presents implementation details and empirical results for a hybrid message passing and shared memory paralleliziation of the adaptive integral method (AIM). AIM is implemented on a (near) petaflop supercomputing cluster of…
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…
In this work, we investigate the potential utility of parallelization for meeting real-time constraints and minimizing energy. We consider malleable Gang scheduling of implicit-deadline sporadic tasks upon multiprocessors. We first show 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…
The AIPC concept is gaining popularity, and more and more hybrid CPUs will be running AI models on client devices. However, the current AI inference framework overlooks the imbalanced hardware capability of hybrid CPUs, leading to low…
Using a realistic molecular catalyst system, we conduct scaling studies of ab initio molecular dynamics simulations using the CP2K code on both Intel Xeon CPU and NVIDIA V100 GPU architectures. We explore using process placement and…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
In this paper, we describe the performance of an $N$-body simulation of star cluster with 64k stars on a Cray XD1 system with 400 dual-core Opteron processors. A number of astrophysical $N$-body simulations were reported in SCxy…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…
Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…
Load balancing is a widely accepted technique for performance optimization of scientific applications on parallel architectures. Indeed, balanced applications do not waste processor cycles on waiting at points of synchronization and data…
Large Language Models (LLMs) continue to demonstrate superior performance with increasing scale, yet training models with billions to trillions of parameters requires staggering computational resources, e.g. a one-trillion-parameter…