LAMMPS strong scaling performance optimization on Blue Gene/Q
Abstract
LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.
- Authors:
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- Argonne National Laboratory - Argonne Leadership Computing Facility
- OSTI Identifier:
- 1164521
- Report Number(s):
- ANL/ALCF-14-3
109821
- DOE Contract Number:
- AC02-06CH11357
- Resource Type:
- Technical Report
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Coffman, Paul, Jiang, Wei, and Romero, Nichols A. LAMMPS strong scaling performance optimization on Blue Gene/Q. United States: N. p., 2014.
Web. doi:10.2172/1164521.
Coffman, Paul, Jiang, Wei, & Romero, Nichols A. LAMMPS strong scaling performance optimization on Blue Gene/Q. United States. https://doi.org/10.2172/1164521
Coffman, Paul, Jiang, Wei, and Romero, Nichols A. 2014.
"LAMMPS strong scaling performance optimization on Blue Gene/Q". United States. https://doi.org/10.2172/1164521. https://www.osti.gov/servlets/purl/1164521.
@article{osti_1164521,
title = {LAMMPS strong scaling performance optimization on Blue Gene/Q},
author = {Coffman, Paul and Jiang, Wei and Romero, Nichols A.},
abstractNote = {LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.},
doi = {10.2172/1164521},
url = {https://www.osti.gov/biblio/1164521},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Nov 12 00:00:00 EST 2014},
month = {Wed Nov 12 00:00:00 EST 2014}
}