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The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…
We present a new adaptive parallel algorithm for the challenging problem of multi-dimensional numerical integration on massively parallel architectures. Adaptive algorithms have demonstrated the best performance, but efficient many-core…
This paper presents an experimental evaluation of parallel-in-time Kalman filters and smoothers using graphics processing units (GPUs). In particular, the paper evaluates different all-prefix-sum algorithms, that is, parallel scan…
We present a scheme for the parallelization of quantum Monte Carlo on graphical processing units, focusing on bosonic systems and variational Monte Carlo. We use asynchronous execution schemes with shared memory persistence, and obtain an…
The main objective of this work consists in analyzing sub-structuring method for the parallel solution of sparse linear systems with matrices arising from the discretization of partial differential equations such as finite element, finite…
Detailed analysis of efficiency and pollutant emission characteristics of practical turbulent combustion devices using complex combustion kinetics often depend on the interactions between the combustion chemistry involving both gasses…
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…
In this paper, we aim to introduce a new perspective when comparing highly parallelized algorithms on GPU: the energy consumption of the GPU. We give an analysis of the performance of linear algebra operations, including addition of…
High fidelity scientific simulations modeling physical phenomena typically require solving large linear systems of equations which result from discretization of a partial differential equation (PDE) by some numerical method. This step often…
Solving inverse problems and achieving statistical rigour in landscape evolution models requires running many model realizations. Parallel computation is necessary to achieve this in a reasonable time. However, no previous algorithm is…
The Poisson equation is critical to get a self-consistent solution in plasma fluid simulations used for Hall effect thrusters and streamer discharges, since the Poisson solution appears as a source term of the unsteady nonlinear flow…
The recent evolution of software and hardware technologies is leading to a renewed computational interest in Particle-In-Cell (PIC) methods such as the Material Point Method (MPM). Indeed, provided some critical aspects are properly…
The problem of Bayesian filtering and smoothing in nonlinear models with additive noise is an active area of research. Classical Taylor series as well as more recent sigma-point based methods are two well-known strategies to deal with these…
Machine learning algorithms are becoming increasingly prevalent and performant in the reconstruction of events in accelerator-based neutrino experiments. These sophisticated algorithms can be computationally expensive. At the same time, the…
Subgraph isomorphism is a well-known NP-hard problem that is widely used in many applications, such as social network analysis and query over the knowledge graph. Due to the inherent hardness, its performance is often a bottleneck in…
We present a matrix-free GPU multigrid preconditioner with algebraically consistent coarsening for solving Poisson equations on adaptive octree grids with irregular domains. Within uniform-resolution regions, the coarsening satisfies the…
We describe the GPU implementation of shifted or multimass iterative solvers for sparse linear systems of the sort encountered in lattice gauge theory. We provide a generic tool that can be used by those without GPU programming experience…
We present a fast and accurate algorithm to solve Poisson problems in complex geometries, using regular Cartesian grids. We consider a variety of configurations, including Poisson problems with interfaces across which the solution is…
We introduce a variant of the Gatenby-Gawlinski model for acid-mediated tumor invasion, accounting for anisotropic and heterogeneous diffusion of the lactic acid across the surrounding healthy tissues. Numerical simulations are performed…
Linear Programs (LPs) appear in a large number of applications and offloading them to a GPU is viable to gain performance. Existing work on offloading and solving an LP on a GPU suggests that there is performance gain generally on large…