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Existing methods of obtaining runtime feedback for structure data-layout optimization have several drawbacks, such as large overhead and difficulty composing training sets. As a result, structure data-layout optimization is not widely used. To overcome these drawbacks, a performance monitoring unit (PMU) sampling method was developed with much less overhead and better portability and usability. An algorithm was developed to correct incomplete and inaccurate PMU sampling. With the corrected PMU feedback, a structure data-layout optimizer achieved a 45.1%performance improvement compared to a design without data-layout optimization, which is 97.6% of the performance improvement achieved with instrumented feedback. Calculation of the PMU feedback increased the execution time by 12.3%, compared to the overhead for the instrumented feedback of 341.5%. Tests show that the PMU feedback is efficient and effective for structure data-layout optimization.