Cleaned up bUseGpu in runner

Cleaned up bUseGpu in runner

This variable was rather unclear about what it actually meant, and
various comments were wrong. This had several effects.

It obscured that automated assignment of GPU IDs to PP ranks actually
does take place after thread-MPI thread launch.

Fixing it revealed that we set up nstlist and rlist for the Verlet
scheme unnecessarily early, and this leads to an extra broadcast
(which is not costly, because there are many other broadcast calls
nearby).

Previously, -nb gpu and -nb auto would trigger GPU detection, and the
result of the detection was used to decide whether GPU assignment
might take place. tryUsePhysicalGpu and forceUsePhysicalGPu now play
the latter role, so that it is clear that we have the flexibility to
avoid assigning work to GPUs when that does not make sense (e.g. rerun
with energy groups), even if GPUs are detected. In particular,
tryUsePhysicalGpu needs to default to false when GPU support is not
configured, and when the .tpr is for the group scheme.

Removed strange comment about ignoring manually selected GPUs, which
may have been an historical artefact about doing so on PME-only ranks.

Change-Id: I69f21210a7ee931e5fa2cbe49e0999ad89ba7426