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Scratchpad Memory (SPM), a software-controlled on-chip memory, has been widely used as an alternative to caches in modern embedded systems due to its energy efficiency. To further reduce the energy consumption, non-volatile memory (NVM) based hybrid SPM has been proposed recently. This paper targets the problem of allocating program variables into hybrid SPM based systems. Both an ILP formulation and a graph-coloring based algorithm are proposed. The experiments show that the proposed graph-coloring framework achieves both better memory latency and lower energy costs in comparison to previous works.