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This paper is concerned with the nonrepeatable runout (NRRO) compensation problem for hard disk drives. After standard servo control, several visible frequency components remain in the spectrum of nonrepeatable position error signal (NRPES). The dominant ones among these frequency components contribute a lot to the track mis-registration (TMR). In this paper, we propose an adaptive compensation scheme for the time-varying dominant frequency component of NRRO. The frequency of the dominant component is estimated online by the least mean squares (LMS) algorithm within a short time window. Based on the frequency estimate, the basis function algorithm is applied to adaptively identify the time-varying magnitude and phase of the dominant component. With the identified frequency, magnitude, and phase, an estimate of the dominant component is constructed and then canceled by the control signal. This scheme is further extended to compensating for multiple frequency components. The performance of this compensation scheme is demonstrated by simulation on a realistic hard disk drive model.