1. A method for configuring a system comprising a plurality of computation units interconnected by an interconnection network using a computer system, the method comprising: accepting, by the computer system, a set of instructions corresponding to a portion of a program that performs a computation repeatedly; identifying subsets of the instructions including associating instructions with the subsets to reduce at least some potential cyclic communication dependency among the computation units; and associating each subset with a different one of the computation units to form a specification of the set of instructions such that execution according to the specification forms a pipeline among at least some of the computation units.