This is an archive of papers published by the staff and faculty of Fox Chase Cancer Center. For questions about content, please contact Talbot Research Library
Last updated on
Gallicchio E , Xia J , Flynn WF , Zhang B , Samlalsingh S , Mentes A , Levy RM
Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing
Comput Phys Commun. 2015 Nov;196 :236-246
PMID: 27103749 PMCID: PMC4834714 URL: https://www.ncbi.nlm.nih.gov/pubmed/27103749
AbstractParallel 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.
NotesGallicchio, Emilio Xia, Junchao Flynn, William F Zhang, Baofeng Samlalsingh, Sade Mentes, Ahmet Levy, Ronald M P50 GM103368/GM/NIGMS NIH HHS/United States R01 GM030580/GM/NIGMS NIH HHS/United States Journal article Comput Phys Commun. 2015 Nov;196:236-246.