Replica exchange is a powerful sampling algorithm that preserves canonical distributions and allows for efficient crossing of high energy barriers that separate thermodynamically stable states. In this algorithm, several copies or replicas, of the system of interest are simulated in parallel at different temperatures using “walkers”. These walkers occasionally swap temperatures and other parameters to allow them to bypass enthalpies barriers by moving to a higher temperature. The replica exchange algorithm has several advantages over formulations based on constant temperature, and has the potential for significantly impacting the fields of structural biology and drug design - specifically, the problems of structure based drug design and the study of the molecular basis of human diseases associated with protein misfolding.

While these replica exchange simulations can definitely benefit from the potentially large numbers of processors available in a Desktop Grid environment, general formulations of the replica exchange algorithm require complex coordination and communication patterns between the walkers. Coupled with the complexity of the Grid environment, including its scale, its heterogeneity in computational, storage and communication capabilities, its dynamism and its unreliability, Grid-based replica exchange simulations present significant challenges. It is probably for this reason that, to the best of our knowledge, all the current parallel/distributed implementations of replica exchange simulations in use by the structural biology community target small homogenous systems. Further, these implementations are based on a simplified formulation of the algorithm that limits the potential power of the technique in two important aspects: (1) the only parameter exchanged between the replicas is the temperature of each replica, and (2) the exchanges occur in a centralized and totally synchronous manner, and only between replicas with adjacent temperatures. The former limits the effectiveness of the method and impedes temperature mixing, while the latter limits its scalability to a small number of homogeneous and relatively tightly coupled processors.

Clearly, the complexity of developing Grid-based replica exchange must be abstracted from the application scientists/engineers and effectively addressed by a computational infrastructure. Such an infrastructure should support dynamic walker management and efficient, robust and scalable exchanges to enable large scale simulations of the structure, function, folding, and dynamics of proteins. This work consists of two components: (1) an asynchronous formulation of replica exchange that is more suited to Grid environments and (2) a Grid-based asynchronous replica exchange engine (GARE). The asynchronous replica exchange formulation builds on our initial algorithm proposed in project Salsa and has the following characteristics: (1) the exchanged parameters and the overall parameter ranges used by the simulation are determined at the beginning of the simulation and are known to all the walkers; (2) the parameters assigned to a walker only change when the walker performs an exchange; (3) exchanges can occur between walkers on different nodes; and (4) the walkers can dynamically join or leave the system. The first two observations allow individual walkers to locally determine the ranges of interest and enable exchange decisions to be made in a decentralized and decoupled manner. The third allows actual exchanges to occur between pairs of walkers in parallel. The last observation enables the replica exchange to deal with the environment and system dynamism.

The Grid-based asynchronous replica exchange engine builds on CometG and ex- tends it to provide the abstractions and mechanisms required by asynchronous replica exchange, including mechanisms for dynamic and anonymous task distribution, task coordination and execution, decoupled communication and data exchange. It provides a virtual shared space abstraction that can be associatively accessed by all walkers with- out knowledge of the physical locations of the hosts over which the space is distributed. The walkers can use this space to dynamically discover exchange partners, negotiate with them, and exchange data. Walkers periodically post temperature ranges that are of current interest for exchange to the space. If this range overlaps with the range of interest posted by another walker, an exchange can occur. The actual exchange is then negotiated and completed by the individual walkers in a peer-to-peer manner. As a result, exchanges are decoupled, dynamically and asynchronously determined, and not limited to neighboring temperatures.

 

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