Quantum computing promises solutions to classically difficult and new-found problems through controlling the subtleties of quantum computing. The Quantum Approximate Optimisation Algorithm (QAOA) is a recently proposed quantum algorithm designed to tackle difficult combinatorial optimisation problems utilising both quantum and classical computation. The hybrid nature, generality and typically low gate-depth make it a strong candidate for near-term implementation in quantum computing. Finding the practical limits of the algorithm is currently an open problem. Until now, no tools to facilitate the design and validation of probabilistic quantum optimisation algorithms such as the QAOA on a non-trivial scale exist. Graph similarity is a long standing classically difficult problem withstanding decades of research from academia and industry. Determining the maximal edge overlap between all possible node label permutations is an NP-Complete task and provides an apt measure of graph similarity. We introduce a novel quantum optimisation simulation package facilitating investigation of all constituent components of the QAOA from desktop to cluster scale using graph similarity as an example. Our simulation provides flexibility and performance. We investigate eight classical optimisation methods each at six levels of decomposition. Moreover an encoding for permutation based problems such as graph similarity through edge overlap to the QAOA allows for significant quantum memory savings at the cost of additional operations. This compromise extends into the classical portion of the algorithm as the inclusion of infeasible solutions creates a challenging cost-function landscape. We present performance analysis of our simulation and of the QAOA setting a precedent for investigating and validating numerous other difficult problems to the QAOA as we move towards realising practical quantum computation.