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A special class of quadratic programming (QP) problems is considered in this paper. This class emerges in simulation of assembly of large-scale compliant parts, which involves the formulation and solution of contact problems. The considered QP problems can have up to 20,000 unknowns, the Hessian matrix is fully populated and ill-conditioned, while the matrix of constraints is sparse. Variation analysis and optimization of assembly process usually require massive computations of QP problems with slightly different input data. The following optimization methods are adapted to account for the particular features of the assembly problem: an interior point method, an active-set method, a Newton projection method, and a pivotal algorithm for the linear complementarity problems. Equivalent formulations of the QP problem are proposed with the intent of them being more amenable to the considered methods. The methods are tested and results are compared for a number of aircraft assembly simulation problems.