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Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

Emilio Gallicchio1, Junchao Xia2, William F Flynn2

  • 1Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, NY.

Computer Physics Communications
|April 23, 2016
PubMed
Summary
This summary is machine-generated.

ASyncRE software enables asynchronous replica exchange molecular simulations on distributed computing grids. This approach overcomes communication barriers, allowing efficient exploration of chemical system conformations on diverse hardware.

Keywords:
BOINCdistributed computinggrid computingpeptide dimerizationprotein-ligand bindingreplica exchange molecular dynamics

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Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Distributed computing

Background:

  • Replica exchange is crucial for exploring molecular conformations but hindered by communication needs on distributed systems.
  • Existing methods face challenges in deploying replica exchange on heterogeneous and volunteered computing resources.

Purpose of the Study:

  • To introduce ASyncRE, a software architecture for asynchronous replica exchange molecular simulations.
  • To enable efficient use of volunteered computing grids and heterogeneous high-performance clusters for molecular simulations.

Main Methods:

  • ASyncRE employs an asynchronous algorithm that eliminates centralized synchronization and direct inter-process communication.
  • The software allows molecular dynamics threads to run at different rates and enables independent parameter exchanges between replicas.
  • ASyncRE is implemented in Python with a modular design for adaptability to various replica exchange schemes and simulation engines.

Main Results:

  • ASyncRE successfully models association equilibria of supramolecular and macromolecular complexes.
  • Demonstrated application on BOINC campus computational grids and the XSEDE Stampede supercomputer (CPU/MIC heterogeneous hardware).
  • Showcased the ability to leverage large grids of desktop computers (Windows, MacOS, Linux) and high-performance heterogeneous hardware.

Conclusions:

  • ASyncRE overcomes deployment limitations of traditional replica exchange on distributed and heterogeneous resources.
  • The software facilitates large-scale molecular simulations by utilizing volunteered and high-performance computing infrastructure.
  • ASyncRE offers a flexible and efficient solution for exploring complex chemical system dynamics.