Joel,

I have code that runs fine with periodic boundary condition for 
> a GridGenerator::parallelepiped. Also when I change the mesh to 
> a GridGenerator::subdivided_parallelepiped and has only 1 as 
> n_subdivisions, it also works. But when I change it to 2, I get the 
> following error:
> [...]
>
GridTools::collect_periodic_faces[1] tries to match the faces on the 
boundaries specified by the two boundary_ids on the coarsest level and here 
finds a face that can't be matched. 
Can you give us a minimal example just creating that mesh and trying to 
compute periodic boundary conditions?
>From just your description, it is hard to say what the problem is, but I 
would not expect that subdividing should be an issue.

Best,
Daniel

[1] 
https://dealii.org/8.4.1/doxygen/deal.II/namespaceGridTools.html#aaeadfc0053429f542fbfd48d192b94f0

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