Parallel and distributed simulation (PDS) is often employed to tackle the computational intensity of system-level simulation of real-world complex embedded and cyber-physical systems (CPSs). However, CPS models comprise heterogeneous components with diverge semantics for which incompatible PDS approaches are developed. We propose an automated PDS flow based on a formal modeling framework—with necessary extensions—targeting heterogeneous embedded and CPS design. The proposed flow characterizes the sequential executable specification of a heterogeneous model and generates a PDS cluster. State-of-the-art graph partitioning methods are adopted and a new extensible constraint-base formulation of the model partitioning problem is developed. The applicability, effectiveness, and scalability of the proposed flow is demonstrated using case studies.