is the example "... waves rumbled across the reef..." a metaphor???

No, but it might be personification. Or maybe onomatopoeia, in a way.

I don't see which two unlike things are being compared.

It looks more like personification.

Yes, the example "waves rumbled across the reef" is a metaphor. A metaphor is a figure of speech that implies a comparison between two things that are not literally alike but share some similar qualities. In this case, the author is comparing the movement of the waves to the sound of rumbling, suggesting that the waves are powerful and forceful in a way that is similar to the rumble of thunder or an earthquake. To determine if a sentence or phrase is a metaphor, you can look for words or phrases that signify a comparison between two unrelated things, such as "like" or "as." In this case, there is no direct use of "like" or "as," but the comparison is still implied through the description of the waves as "rumbling," which is typically associated with sounds rather than physical movement.