Speculation and replication in temperature accelerated dynamics
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Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. Here, we compare the performance of speculative parallelism with a replica-based technique, similar to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.
I. INTRODUCTION
Given the availability of parallel computing resources, it has become more valuable than ever to design atomistic simulation algorithms that are well suited for distributed computing clusters. When it comes to Molecular Dynamics (MD) simulations, algorithm development has mostly focused on improving weak scaling through spatial decomposition. These efforts have been very effective, allowing current researchers to routinely simulate billions of atoms or more.1,2 Unfortunately, spatial decomposition has done very little to extend the maximum temporal reach of MD beyond a few microseconds. This is because MD requires the sequential integration of Newton’s equations, and a femtosecond-scale time step is typically needed to ensure numerical stability. The Accelerated Molecular Dynamics (AMD) approach to the MD time scale problem is to produce a state-wise trajectory at a faster rate than direct MD. It does so by leveraging the separation of time scales between the numerical integration time step and state-to-state transitions. This approach is particularly well suited for applications where this separation is large, like point-defect evolution in crystalline materials. The performance of an AMD algorithm is often expressed in terms of a computational boost factor, given by WCTMD/WCTAMD, where Contributing Editor: Enrique Martinez a) Address all correspondence to this author. e-mail: [email protected] b) This author was an editor of this journal during the review and decision stage. For the JMR policy on review and publication of manuscripts authored by editors, please refer to http://www.mrs. org/editor-manuscripts/. DOI: 10.1557/jmr.2018.17
WCTMD and WCTAMD refer to the required wall clock time (WCT) for direct MD and AMD, respectively. Since the late 1990’s, three generalizations of the AMD approach have been established: Hyperdynamics,3 Parallel Replica Dynamics (PRD),4,5 and TemperatureAccelerated Dynamics (TAD),6 each containing a variety of sub-me
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