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In this paper, we derive set constraints for a reduced order model and augment them into a model predictive control (MPC) scheme to ensure safe operation of the large-scale ensemble system. For the control feedback, only the aggregated information of the whole system is required. For the constraint satisfaction, we consider an adaptive tube formulation to characterize the deviation between the reduced order model and the ensemble system. Employing the robust control invariant set, we ensure recursive feasibility and initial feasibility under an easily verifiable condition.