Related papers: The Tersoff many-body potential: Sustainable perfo…
Traditionally, distributed and parallel transactional systems have been studied in isolation, as they targeted different applications and experienced different bottlenecks. However, modern high-bandwidth networks have made the study of…
In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals…
This study presents the vectorization of metaheuristic algorithms as the first stage of vectorized optimization implementation. Vectorization is a technique for converting an algorithm, which operates on a single value at a time to one that…
In this report we present a network-level multi-core energy model and a software development process workflow that allows software developers to estimate the energy consumption of multi-core embedded programs. This work focuses on a high…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
The study of correlated mutations in alignments of homologous proteins proved to be succesful not only in the prediction of their native conformation, but also in the developement of a two-body effective potential between pairs of amino…
We analyze the properties of particles trapped in three-dimensional potentials formed from superimposed Gaussian beams, fully taking into account effects of potential anharmonicity and non-separability. Although these effects are negligible…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
Accurate hardware performance models are critical to efficient code generation. They can be used by compilers to make heuristic decisions, by superoptimizers as a minimization objective, or by autotuners to find an optimal configuration for…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
Many robot planning tasks require satisfaction of one or more constraints throughout the entire trajectory. For geometric constraints, manifold-constrained motion planning algorithms are capable of planning collision-free path between start…
The ever-growing scale of data parallelism in today's HPC and ML applications presents a big challenge for computing architectures' energy efficiency and performance. Vector processors address the scale-up challenge by decoupling Vector…
This paper is aimed at improving the performance of the treecode algorithm for N-Body simulation by employing the NetSolve GridRPC programming model to exploit the use of multiple clusters. N-Body is a classical problem, and appears in many…
Many-body localization is a striking mechanism that prevents interacting quantum systems from thermalizing. The absence of thermalization behaviour manifests itself, for example, in a remanence of local particle number configurations, a…
Sparse matrix-vector multiplication (SpMV) operations are commonly used in various scientific applications. The performance of the SpMV operation often depends on exploiting regularity patterns in the matrix. Various representations have…
We recently proposed a new variational theory of "tensor-optimized antisymmetrized molecular dynamics" (TOAMD), which treats the strong interaction explicitly for finite nuclei [T. Myo et al., Prog. Theor. Exp. Phys. 2015, 073D02 (2015)].…
Load balancing is a widely accepted technique for performance optimization of scientific applications on parallel architectures. Indeed, balanced applications do not waste processor cycles on waiting at points of synchronization and data…
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 a parallel visualization algorithm for the illustrative rendering of depth-dependent stylized dense tube data at interactive frame rates. While this computation could be efficiently performed on a GPU device, we target a parallel…
Leading HPC systems achieve their status through use of highly parallel devices such as NVIDIA GPUs or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital…