Modifications in classes of RunTime and CPUTime

As Dimm suggested. I subtracted this PR from  #487 specially for classes  of  ``PETScWallClockTimer``, ``RunTime``, and ``CPUTime``. With the modifications in ``RunTime`` and ``CPUTime``, member ``stop()`` was removed. @TomFischer and @endJunction ,please take a look.

PR #487 will be closed temporarily due to the ``reset node ID`` issue, and it will be reopened once a FEM (say for a simple elliptic problem ) is completed in  the official repository. 
i think it's safer if we have it. but i am also not sure because i haven't seen an error saying mpi.h is missing. perhaps mpicxx (or CMake) automatically adds the path to include dir. but this can depend on environment and which MPI library we use.