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DTSTART:19700308T020000
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DTSTAMP:20181221T160731Z
LOCATION:D171/173
DTSTART;TZID=America/Chicago:20181116T084000
DTEND;TZID=America/Chicago:20181116T085500
UID:submissions.supercomputing.org_SC18_sess145_ws_p3hpc103@linklings.com
SUMMARY:High-Performance Molecular Dynamics Simulation for Biological and 
 Materials Sciences: Challenges of Performance Portability
DESCRIPTION:Workshop\nHeterogeneous Systems, Performance, Workshop Reg Pas
 s\n\nHigh-Performance Molecular Dynamics Simulation for Biological and Mat
 erials Sciences: Challenges of Performance Portability\n\nSedova, Eblen, B
 udiardja, Tharrington, Smith\n\nHighly-optimized parallel molecular dynami
 cs programs have, in recent years, allowed researchers to achieve ground-b
 reaking results in biological and materials sciences. This type of perform
 ance has come at the expense of portability: a significant effort is requi
 red for performance optimization on each new architecture. Using a metric 
 that emphasizes speedup and time-to-solution, we analyze the code-bases an
 d performance portabilities of four different high-performing molecular dy
 namics programs-- GROMACS, NAMD, LAMMPS and CP2K--  each having a particul
 ar scope of application. We find that for all four programs, the contribut
 ions 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 m
 agnitude that is insufferable to domain scientists. We discuss possible so
 lutions to this difficult problem, which must come from developers, indust
 ry and funding institutions, and possibly new developments in programming 
 languages.
URL:https://sc18.supercomputing.org/presentation/?id=ws_p3hpc103&sess=sess
 145
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