A GPU-accelerated fast multipole method for GROMACS: performance and accuracy

B Kohnke, C Kutzner… - Journal of Chemical Theory …, 2020 - ACS Publications
An important and computationally demanding part of molecular dynamics simulations is the
calculation of long-range electrostatic interactions. Today, the prevalent method to compute …

Scheduling on two types of resources: a survey

O Beaumont, LC Canon, L Eyraud-Dubois… - ACM Computing …, 2020 - dl.acm.org
The evolution in the design of modern parallel platforms leads to revisit the scheduling jobs
on distributed heterogeneous resources. The goal of this survey is to present the main …

[PDF][PDF] Collaboro: a collaborative (meta) modeling tool

JLC Izquierdo, J Cabot - PeerJ Computer Science, 2016 - peerj.com
Motivation Scientists increasingly rely on intelligent information systems to help them in their
daily tasks, in particular for managing research objects, like publications or datasets. The …

A fast time-domain boundary element method for three-dimensional electromagnetic scattering problems

T Takahashi - Journal of Computational Physics, 2023 - Elsevier
This paper proposes a fast time-domain boundary element method (TDBEM) to solve three-
dimensional transient electromagnetic scattering problems regarding perfectly electric …

From piz daint to the stars: Simulation of stellar mergers using high-level abstractions

G Daiß, P Amini, J Biddiscombe, P Diehl… - Proceedings of the …, 2019 - dl.acm.org
We study the simulation of stellar mergers, which requires complex simulations with high
computational demands. We have developed Octo-Tiger, a finite volume grid-based …

Towards extreme scale technologies and accelerators for eurohpc hw/sw supercomputing applications for exascale: the textarossa approach

G Agosta, M Aldinucci, C Alvarez, R Ammendola… - Microprocessors and …, 2022 - Elsevier
In the near future, Exascale systems will need to bridge three technology gaps to achieve
high performance while remaining under tight power constraints: energy efficiency and …

A visual performance analysis framework for task‐based parallel applications running on hybrid clusters

V Garcia Pinto, L Mello Schnorr… - Concurrency and …, 2018 - Wiley Online Library
Summary Programming paradigms in High‐Performance Computing have been shifting
toward task‐based models that are capable of adapting readily to heterogeneous and …

Application of the inverse fast multipole method as a preconditioner in a 3D Helmholtz boundary element method

T Takahashi, P Coulier, E Darve - Journal of Computational Physics, 2017 - Elsevier
We investigate an efficient preconditioning of iterative methods (such as GMRES) for solving
dense linear systems A x= b that follow from a boundary element method (BEM) for the 3D …

A new approach to latency insensitive design

MR Casu, L Macchiarulo - Proceedings of the 41st Annual Design …, 2004 - dl.acm.org
Latency Insensitive Protocols have been proposed as a viable mean to speed up large
Systems-on-Chip where the limit in clock frequency is given by long global wires connecting …

[PDF][PDF] On runtime systems for task-based programming on heterogeneous platforms

S Thibault - 2018 - inria.hal.science
SIMULATION has become pervasive in science. Real experimentation remains an essential
step in scientific research, but simulation replaced a wide range of costly and lengthy or …