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The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
Graphics Processing Units (GPUs) are having a transformational effect on numerical lattice quantum chromodynamics (LQCD) calculations of importance in nuclear and particle physics. The QUDA library provides a package of mixed precision…
We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate…
Highly-parallel graphics processing units (GPUs) can improve the speed of micromagnetic simulations significantly as compared to conventional computing using central processing units (CPUs). We present a strategy for performing…
Geospatial Processing, such as queries based on point-to-polyline shortest distance and point-in-polygon test, are fundamental to many scientific and engineering applications, including post-processing large-scale environmental and climate…
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…
Hydrodynamics calculations have been successfully used in studies of the bulk properties of the Quark-Gluon Plasma, particularly of elliptic flow and shear viscosity. However, there are areas (for instance event-by-event simulations for…
Graphics Processing Units (GPUs) are becoming popular accelerators in modern High-Performance Computing (HPC) clusters. Installing GPUs on each node of the cluster is not efficient resulting in high costs and power consumption as well as…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Evolutionary computing (EC) has proven to be effective in solving complex optimization and robotics problems. Unfortunately, typical Evolutionary Algorithms (EAs) are constrained by the computational capacity available to researchers. More…
To effectively control large-scale distributed systems online, model predictive control (MPC) has to swiftly solve the underlying high-dimensional optimization. There are multiple techniques applied to accelerate the solving process in the…
In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD)…
iPIC3D is a widely used massively parallel Particle-in-Cell code for the simulation of space plasmas. However, its current implementation does not support execution on multiple GPUs. In this paper, we describe the porting of iPIC3D particle…
Massively multicore processors, such as Graphics Processing Units (GPUs), provide, at a comparable price, a one order of magnitude higher peak performance than traditional CPUs. This drop in the cost of computation, as any…
We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…
The continued growth of the computational capability of throughput processors has made throughput processors the platform of choice for a wide variety of high performance computing applications. Graphics Processing Units (GPUs) are a prime…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
The sizes of GPU applications are rapidly growing. They are exhausting the compute and memory resources of a single GPU, and are demanding the move to multiple GPUs. However, the performance of these applications scales sub-linearly with…
Granular materials are of critical interest to many robotic tasks in planetary science, construction, and manufacturing. However, the dynamics of granular materials are complex and often computationally very expensive to simulate. We…