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With the ever growing complexity of high performance computing (HPC) systems to satisfy emerging application requirements (e.g., high memory bandwidth requirement for machine learning applications), the performance bottleneck in such systems has moved from being computation-centric to be more communication-centric. Silicon photonic interconnection networks have been proposed to address the aggressive communication requirements in HPC systems, to realize higher bandwidth, lower latency, and better energy efficiency. There have been many successful efforts on developing silicon photonic devices, integrated circuits, and architectures for HPC systems. Moreover, many efforts have been made to address and mitigate the impact of different challenges (e.g., fabrication process and thermal variations) in silicon photonic interconnects. However, most of these efforts have focused only on a single design layer in the system design space (e.g., device, circuit or architecture level). Therefore, there is often a gap between what a design technique can improve in one layer, and what it might impair in another one. In this paper, we discuss the promise of cross-layer design methodologies for HPC systems integrating silicon photonic interconnects. In particular, we discuss how such cross-layer design solutions based on cooperatively designing and exchanging design objectives among different system design layers can help achieve the best possible performance when integrating silicon photonics into HPC systems