Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.
Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.
Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, NY.
Emilio
E
Gallicchio
Center for Biophysics and Computational Biology, Institute of Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia PA.
Junchao
J
Xia
Center for Biophysics and Computational Biology, Institute of Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia PA.
William F
WF
Flynn
Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, NY.
Baofeng
B
Zhang
Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, NY.
Sade
S
Samlalsingh
Center for Biophysics and Computational Biology, Institute of Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia PA.
Ahmet
A
Mentes
Center for Biophysics and Computational Biology, Institute of Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia PA.
Ronald M
RM
Levy
BOINC; distributed computing; grid computing; peptide dimerization; protein-ligand binding; replica exchange molecular dynamics