The phrase is a metaphor. Supposedly the machine runs so fast that the resulting friction burns the sand. Here the author is playing on the fact that the verb 'run' can be used to describe both rapid physical movement and machine operation.
Another possible (unintended) interpretation is that the machine runs so hot (generates heat as a result of operation) the resulting heat burns even sand. CPUs generate heat when running, and the faster they run, the more heat (hotter) they produce. That why computers have internal fans and heat sinks, to help distribute the heat which result as a side effect of operation.
I'm sure that's not the intended meaning, because running hot is a negative aspect of computers. You may have seen a negative PC/laptop review that comments on how hot the unit gets when running at peak performance.. People who upgrade their machines for better performance often install bigger or more powerful CPU fans to help with the increased heat.
I don't think it's a particularly good metaphor, either.
