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. 
`_MSC_VER` is defined when you build with the Visual Studio compiler. The value of it is some [version information](http://stackoverflow.com/questions/70013/how-to-detect-if-im-compiling-code-with-visual-studio-2008). `WIN32` is defined on Windows, i.e. in Visual Studio but also in other Windows compilers.