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Title: 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}
}