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A bulk synchronous computation proceeds in phases that are separated by barrier synchronization. For dynamic bulk synchronous computations that exhibit varying phase-wise computational requirements, remapping at run-time is an effective approach to ensure parallel efficiency. This paper introduces a novel remapping strategy for computations whose workload changes can be modeled as a Markov chain. It is shown that optimal remapping cart be formulated as a binary decision process: remap or not at a given synchronizing instant. The optimal strategy is then developed for long lasted computations by employing optimal stopping rules in a stochastic control framework. The existence of optimal controls is established. Necessary and sufficient conditions for the optimality are obtained. Furthermore, a policy iteration algorithm is devised to reduce computational complexity and enhance fast convergence to the desired optimal control.