1. A method of configuring a controller for real time control of an industrial process involving at least one industrial machine, wherein a combined Mixed Logical Dynamic (MLD) system represents an industrial process involving at least one industrial machine, each of at least two MLD subsystems represents a sub-process of the industrial process, the MLD subsystems and the combined MLD system each involve vectors of states, vectors of inputs, vectors of outputs, real auxiliary variables and Boolean auxiliary variables, and are described by a state equation, an output equation and constraints, the at least two subsystems are interconnected via dependent pairs formed by a dependent output of one subsystem and a dependent input of the other subsystem, and independent inputs and outputs of the subsystems are not part of the dependent pairs, the state vector of the combined system is composed of the corresponding vectors of states of the subsystems, the input and output vectors of the combined system are composed of the corresponding independent inputs and outputs of the subsystems, and the auxiliary variables of the combined system comprise the corresponding auxiliary variables of the subsystems, wherein the method comprises merging the MLD subsystems into the MLD system by: replacing each dependent pair by an additional auxiliary real and/or Boolean variable of the combined system, and converting the output equation for the dependent output of each of the subsystems into additional constraints of the combined system using the additional auxiliary real and/or Boolean variables exclusive of the replaced dependent pair.