Related papers: GPU parallel simulation algorithm of Brownian part…
We describe an algorithm to construct an intrinsic Delaunay triangulation of a smooth closed submanifold of Euclidean space. Using results established in a companion paper on the stability of Delaunay triangulations on $\delta$-generic…
We consider two particles performing continuous-time nearest neighbor random walk on $\mathbb Z$ and interacting with each other when they are at neighboring positions. Typical examples are two particles in the partial exclusion process or…
Several classic problems in graph processing and computational geometry are solved via incremental algorithms, which split computation into a series of small tasks acting on shared state, which gets updated progressively. While the…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
We present an alternative GPU acceleration for plane waves pseudopotentials electronic structure codes designed for systems that have small unit cells but require a large number of k points to sample the Brillouin zone as happens, for…
This paper focuses on the parallel implementation of a direct $N$-body method~(particle-particle algorithm) and the application of multiple GPUs for galactic dynamics simulations. Application of a hybrid OpenMP-CUDA technology is considered…
We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant…
Fastest arrival events, where the first among many diffusing particles reaches a target, are central in triggering signal initiation in molecular stochastic systems. Classical approaches to simulate such events rely on full trajectory…
The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a…
We develop an algorithm to solve tridiagonal systems of linear equations, which appear in implicit finite-difference schemes of partial differential equations (PDEs), being the time-dependent Schr\"{o}dinger equation (TDSE) an ideal…
Deep learning (DL) jobs use multi-dimensional parallelism, i.e. combining data, model, and pipeline parallelism, to use large GPU clusters efficiently. Long-running jobs may experience changes to their GPU allocation: (i) resource…
We investigate the usage of a recently introduced noise-cancellation algorithm for Brownian simulations to enhance the precision of measuring transport properties such as the mean-square displacement or the velocity-autocorrelation…
We present a new and simple randomized algorithm for constructing the Delaunay triangulation using nearest neighbor graphs for point location. Under suitable assumptions, it runs in linear expected time for points in the plane with…
In this work, we present an extension of Gaussian process (GP) models with sophisticated parallelization and GPU acceleration. The parallelization scheme arises naturally from the modular computational structure w.r.t. datapoints in the…
Brownian simulations can be used to generate statistics relevant for studying molecular interactions or trafficking. However, the concurrent simulation of many Brownian trajectories at can become computationally intractable. Replacing…
A new parallel algorithm utilizing partitioned global address space (PGAS) programming model to achieve high scalability is reported for particle tracking in direct numerical simulations of turbulent flow. The work is motivated by the…
Sequential robot manipulation tasks require finding collision-free trajectories that satisfy geometric constraints across multiple object interactions in potentially high-dimensional configuration spaces. Solving these problems in real-time…
We present a computational algorithm for computing short range forces between particles. The algorithm has two distinguishing features. First, it is optimized for multi-processor computers, and will use as many processors as are available.…
We have developed a fully parallel C++/MPI based simulation code for variable-density particle-laden turbulent flows. The fluid is represented through a uniform Eulerian staggered grid, while particles are modeled using a Lagrangian…
This paper proposes a GPU-accelerated optimization framework for collision avoidance problems where the controlled objects and the obstacles can be modeled as the finite union of convex polyhedra. A novel collision avoidance constraint is…