Generally, a 'model configuration' refers to the:

• horizontal resolution and type of grid (e.g., rectilinear, curvilinear, nodes)
• vertical resolution and coordinate (e.g., pressure, height/depth, hybrid, eta, sigma, stc.)
• physics employed
• time stepping scheme
• method used to formulate the equations (e.g., finite difference, spectral, finite volume, finite element, ...)
• boundary and initial conditions
• coupling with other models (if any); e.g., slab or fully coupled ocean models; AMIP (Use observed sea surface temperatures as lower boundary); land model)