Hi Dave,
There’s some information on ordering quad/hex meshes in the papers: https://doi.org/10.1137/15M1021325 and https://doi.org/10.1145/3061708. This is much more involved than ordering a triangle/tetrahedron mesh, and isn’t implemented in (old) dolfin, but you could do this to your meshes to make them work.
In dolfinx, we’ve been working on permuting the DoF numbering on each element to avoid the need for ordered meshes. It currently works for continuous polynomial spaces, and other spaces are in development, as the issue tracker link in dokken’s reply says. You can run dolfinx using docker, which is much easier than installing from source; I’d recommend trying this before implementing hex reordering.
Running the following commands will launch a docker container from the current master branch of dolfinx:
docker pull quay.io/fenicsproject/dolfinx:real
docker run -ti --rm quay.io/fenicsproject/dolfinx:real