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. 2015 Nov;196:236-246.
doi: 10.1016/j.cpc.2015.06.010.

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing

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Free PMC article

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing

Emilio Gallicchio et al. Comput Phys Commun. .
Free PMC article

Abstract

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.

Keywords: BOINC; distributed computing; grid computing; peptide dimerization; protein-ligand binding; replica exchange molecular dynamics.

Figures

Figure 1
Figure 1
Schematic diagram of the design of ASyncRE. The ASyncRE Manger runs on a coordination server which also hosts the filesystem where replicas are stored. Each cell represents a replica which can be either in a waiting (“W”) state or running (“R”) state. Replicas in the waiting state can exchange state parameters as illustrated by the arrows at the bottom of the diagram. The ASyncRE manager issues replica executions on a variety of computing devices (top) either directly, or through the BOINC grid Manager.
Figure 2
Figure 2
Side and top view of β-cyclodextrin-heptonoate complex
Figure 3
Figure 3
2D asynchronous REMD results from the BOINC distributed network at Temple University and XSEDE HPC resources: (a) distribution of wall clock times for individual 100ps MD simulations; (b) binding energy distributions; (c) binding free energies at different λ values.
Figure 4
Figure 4
Illustrative conformations of the GCN4 leucine zipper dimer from the 2D BEDAM simulations. (c) and (f) are representative of bound and folded conformations. (a,b,c) Replicas at λ = 1 and, respectively, 417, 397, and 362 K at the end of the simulation. Replicas at λ = 1 above 362 K tend to be dissociated and unfolded. (d,e,f) A replica undergoing a folding and binding event at λ = 1 and 379 K in 0.54 ns (time progresses left to right).
Figure 5
Figure 5
Computed dimerization free energy of the GCN4 peptide at two temperatures as a function of simulation length. Values correspond to a window of 3.1 ns per replica (80 RE cycles) ending at the time indicated.

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