Enable auto thread pinning with thread limiting
Recently the possibility of automated limiting the number of OpenMP
threads was introduced (with PME on the GPU). Note that this could
already happen with very small systems. When not using all hardware
threads, pinning would be disabled and a warning was issued.
Now pinning is enabled an no warnings are issued when the user did
not specify any thread and pinning settings.
Changed "threads" in the mdrun -ntmpi description to "ranks".
Change-Id: I5f5688a4e2d35fdddbae3aeffae256158a13da5c