Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
arXiv:1506.00716 [cs.CE], (2 Jun 2015)
@article{szilard2015tackling,
title={Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS},
author={Szilard, Pall and Abraham, Mark James and Kutzner, Carsten and Hess, Berk and Lindahl, Erik},
year={2015},
month={jun},
archivePrefix={"arXiv"},
primaryClass={cs.CE},
doi={10.1007/978-3-319-15976-8_1}
}
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation – in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.
June 5, 2015 by hgpu
