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Title: High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability

Abstract

Highly-optimized parallel molecular dynamics programs have, in recent years, allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: a significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup and time-to-solution, we analyze the code-bases and performance portabilities of four different high-performing molecular dynamics programs-- GROMACS, NAMD, LAMMPS and CP2K-- each having a particular scope of application. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. We discuss possible solutions to this difficult problem, which must come from developers, industry and funding institutions, and possibly new developments in programming languages.

Authors:
ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)
OSTI Identifier:
1493977
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Conference
Resource Relation:
Conference: International Workshop on Performance, Portability, and Productivity in HPC (P3HPC 2018) - Dallas, Texas, United States of America - 11/16/2018 5:00:00 AM-11/16/2018 5:00:00 AM
Country of Publication:
United States
Language:
English

Citation Formats

Sedova, Ada, Eblen, John D., Budiardja, Reuben, Tharrington, Arnold N., and Smith, Jeremy C. High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability. United States: N. p., 2018. Web.
Sedova, Ada, Eblen, John D., Budiardja, Reuben, Tharrington, Arnold N., & Smith, Jeremy C. High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability. United States.
Sedova, Ada, Eblen, John D., Budiardja, Reuben, Tharrington, Arnold N., and Smith, Jeremy C. Thu . "High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability". United States. https://www.osti.gov/servlets/purl/1493977.
@article{osti_1493977,
title = {High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability},
author = {Sedova, Ada and Eblen, John D. and Budiardja, Reuben and Tharrington, Arnold N. and Smith, Jeremy C.},
abstractNote = {Highly-optimized parallel molecular dynamics programs have, in recent years, allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: a significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup and time-to-solution, we analyze the code-bases and performance portabilities of four different high-performing molecular dynamics programs-- GROMACS, NAMD, LAMMPS and CP2K-- each having a particular scope of application. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. We discuss possible solutions to this difficult problem, which must come from developers, industry and funding institutions, and possibly new developments in programming languages.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2018},
month = {11}
}

Conference:
Other availability
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