Related papers: LAMMPS-KOKKOS: Performance Portable Molecular Dyna…
As exascale systems reach unprecedented concurrency, traditional performance analysis tools struggle with the overhead of massive-scale telemetry. We present an accelerated infrastructure for the hpcanalysis framework that leverages a…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…
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…
Large scale simulations are a key pillar of modern research and require ever-increasing computational resources. Different novel manycore architectures have emerged in recent years on the way towards the exascale era. Performance…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
The explosive growth of Large Language Models (LLMs), such as GPT-4 with 1.8 trillion parameters, demands a fundamental rethinking of data center architecture to ensure scalability, efficiency, and cost-effectiveness. Our work provides a…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
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…
We employ pressure point analysis and roofline modeling to identify performance bottlenecks and determine an upper bound on the performance of the Canonical Polyadic Alternating Poisson Regression Multiplicative Update (CP-APR MU) algorithm…
We present a novel, hardware-agnostic implementation strategy for lattice Boltzmann (LB) simulations, which yields massive performance on homogeneous and heterogeneous many-core platforms. Based solely on C++17 Parallel Algorithms, our…
Large Language Models (LLMs) typically generate outputs token by token using a fixed compute budget, leading to inefficient resource utilization. To address this shortcoming, recent advancements in mixture of expert (MoE) models,…
Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…
The Liquid Argon Time Projection Chamber (LArTPC) technology is widely used in high energy physics experiments, including the upcoming Deep Underground Neutrino Experiment (DUNE). Accurately simulating LArTPC detector responses is essential…
OpenCL is a standard for parallel programming of heterogeneous systems. The benefits of a common programming standard are clear; multiple vendors can provide support for application descriptions written according to the standard, thus…
This article presents the principles, software architecture, and performance analysis of the GPU port of the lattice Boltzmann software library Palabos (J. Latt et al., "Palabos: Parallel lattice Boltzmann solver", Comput. Math. Appl. 81,…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
The applications being developed within the U.S. Exascale Computing Project (ECP) to run on imminent Exascale computers will generate scientific results with unprecedented fidelity and record turn-around time. Many of these codes are based…
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…
The unabated growth in AI workload demands is driving the need for concerted advances in compute, memory, and interconnect performance. As traditional semiconductor scaling slows, high-speed interconnects have emerged as the new scaling…