I am writing a very basic OpenGL C++ program (Linux 64 bits).
In fact, i have 3 programs:
OpenGL is just a standard, and that standard has different implementations. Normally, you'd rely on the implementation provided by your graphics driver, which is obviously going to be using the GPU.
However, most desktop Linux distros also include a software implementation of OpenGL, called Mesa, which is what get used if you don't have video drivers installed that support OpenGL. (It's very rare these days to find any video hardware, even integrated video on the CPU, that doesn't support OpenGL shaders, but on Linux drivers can be an issue and in you're case the VM is not making hardware acceleration available.)
So, the short answer is yes your shaders can run on the CPU, but that may or may not happen, and it may or may not be automatic, it depends on what video drivers (or other OpenGL implementation) you have installed.