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This fixes a bug where Rayleigh's timing files always record the number of timesteps as being the maximum number of iterations specified in main_input. This becomes a problem when the user specifies the maximum walltime. For instance, timing files for 3-minute test run might record 10 million timesteps, rather than a few hundred/thousand.
I've been using this branch for several weeks now to performance test Pleiades. If the testers don't throw an error, I am going to merge without review.