From MPI to OpenSHMEM: Porting LAMMPS

Author

Chunyan Tang, University of Tennessee - KnoxvilleFollow

Date of Award

8-2015

Degree Type

Thesis

Degree Name

Master of Science

Major

Computer Engineering

Major Professor

Jack Dongarra

Committee Members

George Bosilca, Audris Mockus

Abstract

This work details the opportunities and challenges of porting a petascale-capable, MPI-based application LAMMPS to OpenSHMEM. We investigate the major programming challenges stemming from the differences in communication semantics, address space organization, and synchronization operations between the two pro- gramming models. This work provides several approaches to solve those challenges for representative communication patterns in LAMMPS, e.g., by utilizing group synchronization, peer’s buffer status tracking, double buffer strategy and unpacked direct transfer of data. The performance of LAMMPS is evaluated on the Titan HPC system at ORNL. The OpenSHMEM implementations are compared with MPI version in terms of both strong and weak scaling. The results outline that OpenSHMEM provides a rich semantic to implement scalable scientific applications. In addition, the experiments demonstrate that OpenSHMEM can compete with, and often improve on, the optimized MPI implementation.

Recommended Citation

Tang, Chunyan, "From MPI to OpenSHMEM: Porting LAMMPS. " Master's Thesis, University of Tennessee, 2015.
https://trace.tennessee.edu/utk_gradthes/3517