A method includes analyzing a dataflow graph representing data dependencies between operators of a dataflow application to identify a plurality of candidate groups of the operators. Based on characteristics of a given hardware accelerator and the operators of a given candidate group of the plurality of candidate groups, determining whether the operators of the given candidate group are to be combined. In response to determining that the operators of the given candidate group are to be combined, retrieving executable binary code segments corresponding to the operators of the given candidate group, generating a unit of binary code including the executable binary code segments and metadata representing an execution control flow among the executable binary code segments, and dispatching the unit of code to the given hardware accelerator for execution of the unit of code.