Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh
- ORNL
- Temple University
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.
- Research Organization:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). National Center for Computational Sciences (NCCS)
- Sponsoring Organization:
- USDOE Office of Science (SC)
- DOE Contract Number:
- DE-AC05-00OR22725
- OSTI ID:
- 1033155
- Journal Information:
- Computer Physics Communications, Vol. 183, Issue 3; ISSN 0010-4655
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ACCELERATION
ALGORITHMS
BENCHMARKS
COMPARATIVE EVALUATIONS
COMPUTER ARCHITECTURE
COMPUTER-GRAPHICS DEVICES
DISTRIBUTED DATA PROCESSING
EFFICIENCY
ELECTROSTATICS
IMPLEMENTATION
KERNELS
MEMORY MANAGEMENT
PERFORMANCE
PARALLEL PROCESSING