I ran the simulation using the master branch and compared the data with the data provided by the Gallery example. The comparison is available in an attachment on this ticket. During the 2018-08-27 weekly ET meeting, it was agreed that the differences were within reasonable tolerance.
Peter Schaffarczyk and I worked on the test. We ran the test simulation on Peter's cluster and found similar results as previously plotted results. We were able to regenerated most of the figures in the website but not all. We are going to continue to update the website with more info about our simulation, and steps to generate the figures.