Related papers: On Designing Multicore-aware Simulators for Biolog…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
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…
Over the last two decades, scientific workflow management systems (SWfMS) have emerged as a means to facilitate the design, execution, and monitoring of reusable scientific data processing pipelines. At the same time, the amounts of data…
Recent advances in computing architectures and networking are bringing parallel computing systems to the masses so increasing the number of potential users of these kinds of systems. In particular, two important technological evolutions are…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Coupling is a widely used technique in the theoretical study of interacting stochastic processes. In this paper I present an example demonstrating its usefulness also in the efficient computer simulation of such processes. I first describe…
Stochastic process models are now commonly used to analyse complex biological, ecological and industrial systems. Increasingly there is a need to deliver accurate estimates of model parameters and assess model fit by optimizing the timing…
Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging,…
Prior work on Automatically Scalable Computation (ASC) suggests that it is possible to parallelize sequential computation by building a model of whole-program execution, using that model to predict future computations, and then…
Running scientific workflows on a supercomputer can be a daunting task for a scientific domain specialist. Workflow management solutions (WMS) are a standard method for reducing the complexity of application deployment on high performance…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
This paper proposes a form of MPC in which the control variables are moved asynchronously. This contrasts with most MIMO control schemes, which assume that all variables are updated simultaneously. MPC outperforms other control strategies…
Computational Steering, the combination of a simulation back-end with a visualisation front-end, offers great possibilities to exploit and optimise scenarios in engineering applications. Due to its interactivity, it requires fast grid…
Manycore System-on-Chip include an increasing amount of processing elements and have become an important research topic for improvements of both hardware and software. While research can be conducted using system simulators, prototyping…
As transistor counts in a single chip exceed tens of billions, the complexity of RTL-level simulation and verification has grown exponentially, often extending simulation campaigns to several months. In industry practice, RTL simulation is…
One of the current challenges in physically-based simulations, and, more specifically, fluid simulations, is to produce visually appealing results at interactive rates, capable of being used in multiple forms of media. In recent times, a…
This work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performance analysis and include memory management, load balance, and…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Increasing complexity in the power system and the transformation towards a smart grid lead to the necessity of new tools and methods for the development and testing of new technologies. One testing method is co-simulation, which allows…