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This paper presents high performance computing results from applications of the CRAFT CFD® software to complex weapons bay configurations. Several flow control concepts have been developed based on past experience with smaller length-to-depth ratio (L/D) cavities with the intended application being a more complex and longer weapons bay. The goal in this paper is to document work done to build confidence in the modeling capability to evaluate flow control concepts for complex weapons bay configurations. The effects of some fundamental bay geometric changes are examined through Large Eddy Simulations. These simulations are validated against measurements and then used to understand the mechanisms involved. The results demonstrate that the extension of previous generic cavity modeling on shorter bays to the longer geometrically complex bay is not straightforward.