Related papers: Tackling Exascale Software Challenges in Molecular…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
The process of setting up and successfully running Molecular Dynamics Simulations (MDS) is outlined to be incredibly labour and computationally expensive with a very high barrier to entry for newcomers wishing to utilise the benefits and…
This paper presents efforts to improve the hierarchical parallelism of a two scale simulation code. Two methods to improve the GPU parallel performance were developed and compared. The first used the NVIDIA Multi-Process Service and the…
In this article, a new generic higher-order finite-element framework for massively parallel simulations is presented. The modular software architecture is carefully designed to exploit the resources of modern and future supercomputers.…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
This study presents a reconstruction of the Gaussian Beam Tracing solution using CUDA, with a particular focus on the utilisation of GPU acceleration as a means of overcoming the performance limitations of traditional CPU algorithms in…
The upcoming exascale computing systems Frontier and Aurora will draw much of their computing power from GPU accelerators. The hardware for these systems will be provided by AMD and Intel, respectively, each supporting their own GPU…
In the recent years it can be observed increasing popularity of parallel processing using multi-core processors, local clusters, GPU and others. Moreover, currently one of the main requirements the IT users is the reduction of maintaining…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
We leverage physics-embedded differentiable graph network simulators (GNS) to accelerate particulate and fluid simulations to solve forward and inverse problems. GNS represents the domain as a graph with particles as nodes and learned…
Simulation models are widely used in practice to facilitate decision-making in a complex, dynamic and stochastic environment. But they are computationally expensive to execute and optimize, due to lack of analytical tractability. Simulation…
Molecular Dynamics simulations can help scientists to gather valuable insights for physical processes on an atomic scale. This work explores various techniques for SIMD vectorization to improve the pairwise force calculation between…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
GPU architectures have become popular for executing general-purpose programs. Their many-core architecture supports a large number of threads that run concurrently to hide the latency among dependent instructions. In modern GPU…
Efficient parallelization of algorithms on general-purpose GPUs is essential in many areas today. However, it is a non-trivial task for software engineers to utilize GPUs to improve the performance of high-level programs in general.…
We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…
Motion planning is a key aspect of robotics. A common approach to address motion planning problems is trajectory optimization. Trajectory optimization can represent the high-level behaviors of robots through mathematical formulations.…