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Nature Computational Science

Opportunities in full-stack design of low-overhead fault-tolerant quantum computation

Hengyun Zhou, Madelyn Cain, Mikhail D. Lukin

Published Dec 22, 2025• 2 citations
Publisher
DOI
10.1038/s43588-025-00895-6

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To run a practical size of quantum program, computer architects have been making tremendous efforts to realize fault-tolerant quantum computing (FTQC) which constructs a fault-tolerant logical qubit by correcting many erroneous physical qubits during runtime. However, it is extremely challenging to build a full-stack FTQC system consisting of heterogeneous stacks, where each stack incurs unique challenges regarding the fault tolerance and the interplay of the challenges incurs very complicated overall design choice problem. Therefore, computer architects must fully understand stack-specific optimizations and their system-level trade-offs, and resolve all the challenges together. In this article, we first introduce critical design challenges in architecting an FTQC system built on the superconducting technology, and then present our research outcomes to resolve the challenges to build an FTQC system realizing thousands of logical qubits. We also outline near-future directions to resolve the remaining challenges and provide insights toward realizing more scalable future FTQC systems.
Scalable quantum computation is expected to rely on fault-tolerant quantum computation (FTQC), in which quantum error correction (QEC) suppresses physical errors sufficiently to support reliable logical operations. This requires quantum compilation to move beyond general-purpose circuit optimization toward encoding-aware and protocol-structured compilation across the full stack of fault-tolerant quantum computers. Beyond circuit synthesis and hardware mapping, an FTQC compiler must lower algorithm-level operations into the logical gate set supported by the chosen code, coordinate encoded data and ancilla resources, realize logical operations together with repeated syndrome extraction under hardware constraints, and provide the resulting measurement stream to real-time decoding. This survey presents a full-stack view of compiler design for QEC-protected quantum computation. We organize existing work into three interacting layers: logical-level QEC compilation, physical-level QEC realization, and decoder runtime integration. At the logical level, we review surface-code lattice-surgery compilers, beyond-surface-code code-surgery frameworks including emerging qLDPC approaches, and compilation support for non-Clifford operations such as magic-state distillation and code switching. At the physical level, we survey hardware-aware QEC realization on superconducting, trapped-ion, and neutral-atom platforms. We further examine decoder models, real-time decoding systems, and frame-management mechanisms that close the feedback loop during fault-tolerant execution. Finally, we identify open challenges in cross-layer optimization, qLDPC compilation, compiler-decoder co-design, runtime adaptivity, and the development of integrated and benchmarkable FTQC compilation stacks. An actively maintained paper list is available at: github.com/chenghongz/QEC-compiler-design.