Related papers: Tackling Exascale Software Challenges in Molecular…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Granular materials are of critical interest to many robotic tasks in planetary science, construction, and manufacturing. However, the dynamics of granular materials are complex and often computationally very expensive to simulate. We…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Among the algorithms that are likely to play a major role in future exascale computing, the fast multipole method (FMM) appears as a rising star. Our previous recent work showed scaling of an FMM on GPU clusters, with problem sizes in the…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
As an important application of spatial databases in pathology imaging analysis, cross-comparing the spatial boundaries of a huge amount of segmented micro-anatomic objects demands extremely data- and compute-intensive operations, requiring…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Exascale computers will offer transformative capabilities to combine data-driven and learning-based approaches with traditional simulation applications to accelerate scientific discovery and insight. These software combinations and…
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. Although the transition from petaflops to exascale computing has been marked by a steady increase in computational…
Turning the current experimental plasma accelerator state-of-the-art from a promising technology into mainstream scientific tools depends critically on high-performance, high-fidelity modeling of complex processes that develop over a wide…
XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The…
This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used…
An early-stage version of simulation package is developed for electronic structure calculation and dynamics of atom process in large-scale systems, particularly, nm-scale or 10nm-scale systems. We adopted the Extensible Markup Language…