Silicon Photonics is emerging as a key technology for highperformance computing interconnects. Yet few tools are available to investigate how to best leverage this technology in current or future computer architectures and, furthermore, how this technology will impact real application workloads. In this paper, we present a multi-layer simulation and modeling software solution -PhoenixSim. PhoenixSim enables integrated and interactive design space exploration over the physical, networking and application layers. In this paper, we report its general organization and constituting models. We show how the different layers of the tool can be utilized to design and analyze an optical interconnect network for supporting the HPCG (High Performance Conjugate Gradient) benchmark.