Abstract
The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. In this paper, we present a continuation of previous work implementing algorithms for using accelerators into the LAMMPS molecular dynamics software for distributed memory parallel hybrid machines. In our previous work, we focused on acceleration for short-range models with an approach intended to harness the processing power of both the accelerator and (multi-core) CPUs. To augment the existing implementations, we present an efficient implementation of long-range electrostatic force calculation for molecular dynamics. Specifically, we present an implementation of the particle-particle particle-mesh method based on the work by Harvey and De Fabritiis. We present benchmark results on the Keeneland InfiniBand GPU cluster. We provide a performance comparison of the same kernels compiled with both CUDA and OpenCL. We discuss limitations to parallel efficiency and future directions for improving performance on hybrid or heterogeneous computers.
| Original language | English |
|---|---|
| Pages (from-to) | 449-459 |
| Number of pages | 11 |
| Journal | Computer Physics Communications |
| Volume | 183 |
| Issue number | 3 |
| DOIs | |
| State | Published - Mar 2012 |
Funding
This research was conducted in part under the auspices of the Office of Advanced Scientific Computing Research , Office of Science, U.S. Department of Energy under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC . This research used resources of the Leadership Computing Facility at Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC. Accordingly, the U.S. Government retains a non-exclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. Sandia is a multipurpose laboratory operated by Sandia Corporation, a Lockheed–Martin Co., for the U.S. Department of Energy under Contract No. DE-AC04-94AL85000. The work was supported in part by the National Science Foundation through grant number CHE-09-46358 and computer time on the Keeneland initial delivery system hosted at the National Institute for Computational Science under grant number UT-NTNL0039 . All of the code described in this paper is available in the open-source LAMMPS software package, available at http://lammps.sandia.gov/ .
Keywords
- Electrostatics
- GPU
- Hybrid parallel computing
- Molecular dynamics
- Particle mesh