Related papers: Breaking Down the Parallel Performance of GROMACS,…
In this paper we study from a numerical analysis perspective the Fractional Step Kinetic Monte Carlo (FS-KMC) algorithms proposed in [1] for the parallel simulation of spatially distributed particle systems on a lattice. FS-KMC are…
The process of setting up and successfully running Molecular Dynamics Simulations (MDS) is outlined to be incredibly labour and computationally expensive with a very high barrier to entry for newcomers wishing to utilise the benefits and…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at…
Nowadays, several industrial applications are being ported to parallel architectures. These applications take advantage of the potential parallelism provided by multiple core processors. Many-core processors, especially the GPUs(Graphics…
FFT (fast Fourier transform) plays a very important role in many fields, such as digital signal processing, digital image processing and so on. However, in application, FFT becomes a factor of affecting the processing efficiency, especially…
In order to run Computational Fluid Dynamics (CFD) codes on large scale infrastructures, parallel computing has to be used because of the computational intensive nature of the problems. In this paper we investigate the ADAPT platform where…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
We propose a simulation-based approach for performance modeling of parallel applications on high-performance computing platforms. Our approach enables full-system performance modeling: (1) the hardware platform is represented by an abstract…
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…
Parallel implementation features of self-gravitating gas dynamics modeling on multiple GPUs are considered applying the GPU-Direct technology. The parallel algorithm for solving of the self-gravitating gas dynamics problem based on hybrid…
The work presented in this paper aims at restricting the input parameter values of the semi-analytical model used in GALICS and MOMAF, so as to derive which parameters influence the most the results, e.g., star formation, feedback and halo…
In this paper, we describe the architecture and performance of the GraCCA system, a Graphic-Card Cluster for Astrophysics simulations. It consists of 16 nodes, with each node equipped with 2 modern graphic cards, the NVIDIA GeForce 8800…
Computational Fluid Dynamics (CFD) is the simulation of fluid flow undertaken with the use of computational hardware. The underlying equations are computationally challenging to solve and necessitate high performance computing (HPC) to…
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…
Cardiovascular disease affects millions of people worldwide and its social and economic cost clearly motivates scientific research. Computer simulation can lead to a better understanding of cardiac physiology, and for pathology presents…
In this paper, we use multithreaded fast Fourier transforms provided in three highly optimized packages, FFTW-2.1.5, FFTW-3.3.7, and Intel MKL FFT, to present a novel model-based parallel computing technique as a very effective and portable…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
We present a parallel implementation of the particle-particle/particle-mesh (P3M) algorithm for distributed memory clusters. The GRACOS (GRAvitational COSmology) code uses a hybrid method for both computation and domain decomposition.…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…