Related papers: A GPU Poisson-Fermi Solver for Ion Channel Simulat…
In this paper we solve on GPUs massive problems with large amount of data, which are not appropriate for solution with the SIMD technology. For the given problem we consider a three-level parallelization. The multithreading of CPU is used…
Numerical solution of partial differential equations on parallel computers using domain decomposition usually requires synchronization and communication among the processors. These operations often have a significant overhead in terms of…
Relativistic fluid dynamics is a major component in dynamical simulations of the quark-gluon plasma created in relativistic heavy-ion collisions. Simulations of the full three-dimensional dissipative dynamics of the quark-gluon plasma with…
High-fidelity simulations of unsteady fluid flow are now possible with advancements in high-performance computing hardware and software frameworks. Since computational fluid dynamics (CFD) computations are dominated by linear algebraic…
Despite decades of research, creating accurate, robust, and efficient lattice Boltzmann methods (LBM) on non-uniform grids with seamless GPU acceleration remains challenging. This work introduces a novel strategy to address this challenge…
We present the development and benchmarking of Poisson solvers for graphics processing units (GPUs). Implemented in the Astaroth platform, the solvers feature high computational efficiency. We present novel combinations of discretizations…
There exists an increasing interest for using immersed boundary methods (IBMs) (Peskin 2000) to model moving objects in computational fluid dynamics. Indeed, this approach is particularly efficient, because the fluid mesh does not require…
A fast Poisson solver software package PoisFFT is presented. It is available as a free software licensed under the GNU GPL license version 3. The package uses the fast Fourier transform to directly solve the Poisson equation on a uniform…
The geometric multigrid method (GMG) is one of the most efficient solving techniques for discrete algebraic systems arising from elliptic partial differential equations. GMG utilizes a hierarchy of grids or discretizations and reduces the…
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,…
Leveraging Graphics Processing Units (GPUs) to accelerate scientific software has proven to be highly successful, but in order to extract more performance, GPU programmers must overcome the high latency costs associated with their use. One…
GPUs have significantly accelerated first-order methods for large-scale optimization, especially in continuous optimization. However, this success has not transferred cleanly to problems with discrete variables, combinatorial structure, and…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
Current supercomputers often have a heterogeneous architecture using both CPUs and GPUs. At the same time, numerical simulation tasks frequently involve multiphysics scenarios whose components run on different hardware due to multiple…
This paper is devoted to computational algorithms designed to describe the classical Ising magnet in some specific cases when an additional macroscopic restriction in form of constant charge density exists in the system. We developed and…
Running kinetic plasma physics simulations using grid-based solvers is very demanding both in terms of memory as well as computational cost. This is primarily due to the up to six-dimensional phase space and the associated unfavorable…
We discuss the efficiency of parallelization on graphical processing units (GPUs) for the simulation of the one dimensional Potts model with long range interactions via parallel tempering. We investigate the behaviour of some thermodynamic…
Gaussian Processes have become an indispensable part of the spatial statistician's toolbox but are unsuitable for analyzing large dataset because of the significant time and memory needed to fit the associated model exactly. Vecchia…
The reliability of cardiovascular computational models depends on the accurate solution of the hemodynamics, the realistic characterization of the hyperelastic and electric properties of the tissues along with the correct description of…