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Abstract: This work is dedicated to the presentation of a matrix-free method for global linear stability analysis in geometries composed of multi-connected rectangular subdomains. An Arnoldi technique using snapshots in subdomains of the entire geometry combined with a multidomain linearized Direct Numerical Finite difference simulations based on an influence matrix for partitioning are adopted. The method is illustrated by three benchmark problems: the lid-driven cavity, the square cylinder and the open cavity flow. The efficiency of the method to extract large-scale structures in a multidomain framework is emphasized. The possibility to use subset of the full domain to recover the perturbation associated with the entire flow field is also highlighted. Such a method appears thus a promising tool to deal with large computational domains and three-dimensionality within a parallel architecture. [Copyright &y& Elsevier]