SpiNNaker is an unconventional supercomputer architecture designed to simulate up to one billion biologically realistic neurons in real-time. To achieve this goal, SpiNNaker employs a novel network architecture which poses a number of practical problems in scaling up from desktop prototypes to machine room filling installations.SpiNNaker's hexagonal torus network topology has received mostly theoretical treatment in the literature. This thesis tackles some of the challenges encountered when building `real-world' systems. Firstly, a scheme is devised for physically laying out hexagonal torus topologies in machine rooms which avoids long cables; this is demonstrated on a half-million core SpiNNaker prototype. Secondly, to improve the performance of existing routing algorithms, a more efficient process is proposed for finding (logically) short paths through hexagonal torus topologies. This is complemented by a formula which provides routing algorithms with greater flexibility when finding paths, potentially resulting in a more balanced network utilisation.The scale of SpiNNaker's network and the models intended for it also present their own challenges. Placement and routing algorithms are developed which assign processes to nodes and generate paths through SpiNNaker's network. These algorithms minimise congestion and tolerate network faults. The proposed placement algorithm is inspired by techniques used in chip design and is shown to enable larger applications to run on SpiNNaker than the previous state-of-the-art. Likewise the routing algorithm developed is able to tolerate network faults, inevitably present in large-scale systems, with little performance overhead.