相关论文: A Parallel and Highly-Portable HPC Poisson Solver:…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
The Poisson pressure solve resulting from the spectral element discretization of the incompressible Navier-Stokes equation requires fast, robust, and scalable preconditioning. In the current work, a parallel scaling study of…
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
With the appearance of the heterogeneous platform OpenPower,many-core accelerator devices have been coupled with Power host processors for the first time. Towards utilizing their full potential, it is worth investigating performance…
Vico et al. (2016) suggest a fast algorithm for computing volume potentials, beneficial to fields with problems requiring the solution of the free-space Poisson's equation, such as beam and plasma physics. Currently, the standard is the…
We consider the problem of computing reachability probabilities: given a Markov chain, an initial state of the Markov chain, and a set of goal states of the Markov chain, what is the probability of reaching any of the goal states from the…
We present a scalable parallel solver for numerical constraint satisfaction problems (NCSPs). Our parallelization scheme consists of homogeneous worker solvers, each of which runs on an available core and communicates with others via the…
Multiphase compressible flows are often characterized by a broad range of space and time scales. Thus entailing large grids and small time steps, simulations of these flows on CPU-based clusters can thus take several wall-clock days.…
This paper presents a large-scale parallel solver, specifically designed to tackle the challenges of solving high-dimensional and high-contrast linear systems in heat transfer topology optimization. The solver incorporates an interpolation…
Realistic reservoir simulation is known to be prohibitively expensive in terms of computation time when increasing the accuracy of the simulation or by enlarging the model grid size. One method to address this issue is to parallelize the…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
We present a parallel implementation of a direct solver for the Poisson's equation on extreme-scale supercomputers with accelerators. We introduce a chunked-pencil decomposition as the domain-decomposition strategy to distribute work among…
Implicit integration of the viscous term can significantly improve performance in computational fluid dynamics for highly viscous fluids such as lava. We show improvements over our previous proposal for semi-implicit viscous integration in…
This paper presents our work on designing scalable linear solvers for large-scale reservoir simulations. The main objective is to support implementation of parallel reservoir simulators on distributed-memory parallel systems, where MPI…
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…
We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences.…
We present a GPU-accelerated version of a high-order discontinuous Galerkin discretization of the unsteady incompressible Navier-Stokes equations. The equations are discretized in time using a semi-implicit scheme with explicit treatment of…
Principal component analysis (PCA) is a key statistical technique for multivariate data analysis. For large data sets the common approach to PCA computation is based on the standard NIPALS-PCA algorithm, which unfortunately suffers from…