Introduced MPI initialization counter

Introduced MPI initialization counter

Normal GROMACS code needs to initialize and finalize MPI. Code that
uses GROMACS as a client (e.g. external code, possible GROMACS test
code) needs GROMACS to work normally and not make erroneous calls to
the MPI library. For example, this would allow a single test binary
to call MPI-enabled mdrun repeatedly to test a range of test cases.

Change-Id: I546518923561a13e3973f90182fa31129ab1e6ae