In 2012, physicists at the University of Bonn suggested a possible way to prove whether we are living in a simulation. A simulation is inherently limited. According to an interview with Silas Beane, one of the researchers:

"In our universe the laws of physics are the same in every direction. But in a grid, this changes since you no longer have a spacetime continuum, and the laws of physics would depend on direction. Simulators would be able to hide this effect but they wouldn’t be able to get rid of it completely."

So, build a simulation of the universe, and see whether that simulation share the exact same properties (such as the variations of cosmic rays) as your universe. If it does, then you have proof that we living are in a simulation. And if you are unable to detect this effect, then the simulation hypothesis is to likely to be rejected as being implausible. The irony of building ancestor-simulations to determine whether we're in an ancestor-simulation is better left unsaid.