Parallel EDMD Simulation on Multi-Core Architectures

Umut DemirtaƟ and Fatih E. Sevilgen

Keywords

Parallel simulation, molecular dynamics, event based simulation, event based molecular dynamics, lock-free lists, event queue

Abstract

Event Driven Molecular Dynamics (EDMD) simulations is an important tool for simulating particle based real systems. Dependency between events causes coherence and causality problems in parallel EDMD simulations. In this paper, we propose a novel parallel EDMD simulation on multi-core architectures. In our method, master-worker strategy is used and a lock-free sorted list structure is implemented as a buffer. We simplify the coherence and causality problems and eliminate most of the locking mechanism. In the algorithm, worker threads get events from an event queue and execute them asynchronously. The results are recorded in the buffer. Master-thread consumes the buffer and then it updates the system state and finally it updates the event queue. Locking mechanism is (still) used to harmonize concurrent access on the event queue. We obtain very promising preliminary experimental results of an ongoing research. On a quad-core computer, speedup of over two times is achieved even for small size systems (32000 molecules).

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