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The results should be identical. The reason you're getting different results is that GPU version of SURF has different default parameters in its constructor than those of CPU SURF

The results should be identical. The reason you're getting different results is that GPU version of SURF has different default parameters in its constructor than those of CPU SURFSURF or maybe you ran into the same bug as I did http://answers.opencv.org/question/87165/surf-on-cuda-every-execution-produces-different-weird-results-for-some-images/