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This paper describes the first steps towards the development of a modelling method for large complex computing systems focusing on many-core types and concentrating on the cross-layer aspects. The models resulting from this method will help system designers reason about, analyse, and ultimately design such systems across all conventional computing and communication layers, from application, operating system, down to the finest hardware details. The main points of concern are energy and power and the physical parameters related to them, such as supply voltages and temperature, among other things, and how these impact on and relate to system"performance" metrics, including speed, throughput, and crucially, reliability. In this paper, we will first establish our outlook for the general modelling method, and then develop an initial system simulator based on this methodological outlook. The simulator will then be demonstrated with an example case study.