3139

General-purpose molecular dynamics simulations on GPU-based clusters

Christian R. Trott, Lars Winterfeld, Paul S. Crozier
Institut fur Physik, University of Technology Ilmenau, 98684 Ilmenau, Germany
arXiv:1009.4330v2 [cond-mat.mtrl-sci] (6 Mar 2011)

@article{2010arXiv1009.4330T,

   title={“{General-purpose molecular dynamics simulations on GPU-based clusters}”},

   author={Trott}, C.~R. and {Winterfeld}, L. and {Crozier}, P.~S.},

   journal={Arxiv preprint arXiv:1009.4330},

   archivePrefix={“arXiv”},

   eprint={1009.4330},

   primaryClass={“cond-mat.mtrl-sci”},

   keywords={Condensed Matter – Materials Science, Computer Science – Distributed, Parallel, and Cluster Computing, Computer Science – Performance, Physics – Computational Physics},

   year={2010},

   month={sep},

   adsurl={http://adsabs.harvard.edu/abs/2010arXiv1009.4330T},

   adsnote={Provided by the SAO/NASA Astrophysics Data System}

}

Download Download (PDF)   View View   Source Source   Source codes Source codes

624

views

We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables multi-GPU simulation on hybrid heterogeneous clusters, using MPI for inter-node communication, CUDA kernels on the GPU for all methods working with particle data, and standard LAMMPS C++ code for CPU execution. Cell and neighbor list approaches are compared for best performance on GPUs, with thread-per-atom and block-per-atom neighbor list variants showing best performance at low and high neighbor counts, respectively. Computational performance results of GPU-enabled LAMMPS are presented for a variety of materials classes (e.g. biomolecules, polymers, metals, semiconductors), along with a speed comparison versus other available GPU-enabled MD software. Finally, we show strong and weak scaling performance on a CPU/GPU cluster using up to 128 dual GPU nodes.
No votes yet.
Please wait...

* * *

* * *

HGPU group © 2010-2017 hgpu.org

All rights belong to the respective authors

Contact us: