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In the face of lower margins, stiffer competition, and ever more stringent product and environmental specifications, petroleum refineries have increasingly relied on optimization approaches to maintain their survival and competitive edge. In this paper, we present a comprehensive overview of the current state of the art role of optimization methods in refineries for wide-ranging multiscale applications and activities spanning the traditional planning linear programming to supply chain that extends to outside-the-fence considerations. The paper aims to provide an integrated treatment of techniques and tools, and a survey of representative work in the burgeoning literature of this field with an emphasis on comparisons between industrial practices and academic research.