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A numerical computer model, based on the dual reciprocity boundary element method (DRBEM) for studying the generalized magneto-thermo-visco-elastic stress waves in a rotating functionally graded anisotropic thin film/substrate structure under pulsed laser irradiation is established. An implicit-implicit staggered algorithm was proposed and implemented for use with the DRBEM to get the solution for the temperature, displacement components and thermal stress components through the structure thickness. A comparison of the results for different theories is presented in the presence and absence of rotation. Some numerical results that demonstrate the validity of the proposed method are also presented.