New class PETScWallClockTimer and 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. 
the option is not used like ogs5 anymore. In OGS5, `OGS_USE_MPI` is used to sepcify certain linear solver using MPI. it made sense at that time because there was only one linear solve using MPI. However, nowadays more than one solvers (petsc, lis, pardiso) are availalbe with MPI and the option name became unspecific. Therefore, in ogs6, i suggest use the flag as its name suggests, i.e. telling wheter we use MPI for paralleization or not. If you are thinking to add the MPI linear solver stuff from ogs5 to ogs6, I would suggest to add new option having meaningful name.