Peter Wegmann, Aleksandra Świerkowska, Emmanouil Giortamis, Pramod Bhatotia

As quantum computing advances toward fault-tolerance through quantum error correction, modular chiplet architectures have emerged to provide the massive qubit counts required while overcoming fabrication limits of monolithic chips. However, this transition introduces a critical compilation gap: existing frameworks cannot handle the scale of fault-tolerant quantum circuits while managing the noisy, sparse interconnects of chiplet backends. We present Chipmunq, the first hardware-aware compiler for mapping and routing fault-tolerant circuits onto modular architectures. Chipmunq employs a quantum-error-correction-aware partitioning strategy that preserves the integrity of logical qubit patches, preventing prohibitive gate overheads common in general-purpose compilers. Our evaluation demonstrates that Chipmunq achieves a 13.5x speedup in compilation time compared to state-of-the-art tools. By incorporating chiplet constraints and defective qubits, it reduces circuit depth by 86.4% and SWAP gate counts by 91.4% across varying code distances. Crucially, Chipmunq overcomes heterogeneous inter-chiplet links, improving logical error rates by up to two orders of magnitude.