A system comprises a plurality of computation units interconnected by an interconnection network. A method for configuring the system comprises receiving an initial partitioning of instructions into initial subsets corresponding to different portions of a program; forming a refined partitioning of the instructions into refined subsets each including one or more of the initial subsets, including determining whether to combine a first subset and a second subset to form a third subset according to a comparison of a communication cost between the first subset and second subset and a load cost of the third subset that is based at least in part on a number of instructions issued per cycle by a computation unit; and assigning each refined subset of instructions to one of the computation units for execution on the assigned computation unit.