Comment (by Roland Haas):

HDF5 builds a couple of utility programs that link against HDF5 (and this MPI if parallel HDF5 is used). So it should run into this same problem (and possibly uses the same sort of ad-hoc solution).

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Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2969/externallibraries-petsc-link-hwloc-into