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For complex engineering and scientific applications, Computational Fluid Dynamics (CFD) simulations require a huge amount of computational power. As such, it is of paramount importance to carefully assess the performance of CFD codes and to study them in depth for enabling optimisation and portability. In this paper, we study three complex CFD codes, OpenFOAM, Alya and CHORUS representing two numerical methods, namely the finite volume and finite-element methods, on both structured and unstructured meshes. To all codes, we apply a generic performance analysis method based on a set of metrics helping the code developer in spotting the critical points that can potentially limit the scalability of a parallel application. We show the root cause of the performance bottlenecks studying the three applications on the MareNostrum4 supercomputer. We conclude providing hints for improving the performance and the scalability of each application. [ABSTRACT FROM AUTHOR]