Related papers: Enhanced molecular dynamics performance with a pro…
We present a new parallel algorithm for probabilistic graphical model optimization. The algorithm relies on data-parallel primitives (DPPs), which provide portable performance over hardware architecture. We evaluate results on CPUs and GPUs…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
The pace of improvement in the performance of conventional computer hardware has slowed significantly during the past decade, largely as a consequence of reaching the physical limits of manufacturing processes. To offset this slowdown, new…
Graphics Processing Units (GPUs) are now powerful and flexible systems adapted and used for other purposes than graphics calculations (General Purpose computation on GPU -- GPGPU). We present here a prototype to be integrated into…
The graphics processing unit (GPU) has emerged as a powerful and cost effective processor for general performance computing. GPUs are capable of an order of magnitude more floating-point operations per second as compared to modern central…
We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU…
Graphics Processing Units (GPUs) support dynamic voltage and frequency scaling (DVFS) in order to balance computational performance and energy consumption. However, there still lacks simple and accurate performance estimation of a given GPU…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
We provide a preliminary study on utilizing GPU (Graphics Processing Unit) to accelerate computation for three simulation optimization tasks with either first-order or second-order algorithms. Compared to the implementation using only CPU…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
Interactive high-performance computing is doubtlessly beneficial for many computational science and engineering applications whenever simulation results should be visually processed in real time, i.e. during the computation process.…
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…
High-performance graphical processing units (GPU) are used for the repeated parallelised propagation of non-linear partial differential equations on large spatio-temporal grids. The main challenge results as a combination of the requirement…
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…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
We carry out a comparative performance study of multi-core CPUs, GPUs and Intel Xeon Phi (Many Integrated Core - MIC) with a microscopy image analysis application. We experimentally evaluate the performance of computing devices on core…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
It is known that quantum computers, if available, would allow an exponential decrease in the computational cost of quantum simulations. We extend this result to show that the computation of molecular properties (energy derivatives) could…
Analog computers can be revived as a feasible technology platform for low precision, energy efficient and fast computing. We justify this statement by measuring the performance of a modern analog computer and comparing it with that of…
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…