Early modular fault tolerant quantum computers remain constrained by costly inter-module communication and limited magic state factory service. Understanding such bottlenecks and investigating compiler optimizations most close the gap between algorithm requirements and hardware capabilities is a concrete and practically urgent systems problem. We study the modular architectures based on Bivariate Bicycle codes and identify the dominant bottleneck: inter-module communication induced by non-Clifford operations. We build a compilation pipeline to fill the missing parts of prior works and propose compiler optimizations: synthesizing arbitrary-angle rotations at the factory (syn@fac), transvection based Clifford deferral, and Clifford insertion for critical path duration reduction. We extend the evaluation scope of the prior work to 40+ benchmark categories drawn from PennyLane and MQTBench, including quantum algorithms and Hamiltonian simulations with varying sizes. Under the present instruction cost, syn@fac reduces estimated circuit failure probability by a factor of 9.0 on average across non-Clifford benchmarks. The robustness persists across sweeps of instruction cost ratios, LPU count, and factory count. Besides, transvection reduces Clifford deferral compile time by 77.04\%, while Clifford insertion reduces end-to-end circuit duration by 11.54\% on average on MQTBench, with smaller gains on Hamiltonian simulations. We hope this work inspires the studies on compiler optimizations for early modular FTQC systems.
Early modular fault tolerant quantum computers remain constrained by costly inter-module communication and limited magic state factory service. Understanding such bottlenecks and investigating compiler optimizations most close the gap between algorithm requirements and hardware capabilities is a concrete and practically urgent systems problem. We study the modular architectures based on Bivariate Bicycle codes and identify the dominant bottleneck: inter-module communication induced by non-Clifford operations. We build a compilation pipeline to fill the missing parts of prior works and propose compiler optimizations: synthesizing arbitrary-angle rotations at the factory (syn@fac), transvection based Clifford deferral, and Clifford insertion for critical path duration reduction. We extend the evaluation scope of the prior work to 40+ benchmark categories drawn from PennyLane and MQTBench, including quantum algorithms and Hamiltonian simulations with varying sizes. Under the present instruction cost, syn@fac reduces estimated circuit failure probability by a factor of 9.0 on average across non-Clifford benchmarks. The robustness persists across sweeps of instruction cost ratios, LPU count, and factory count. Besides, transvection reduces Clifford deferral compile time by 77.04%, while Clifford insertion reduces end-to-end circuit duration by 11.54% on average on MQTBench, with smaller gains on Hamiltonian simulations. We hope this work inspires the studies on compiler optimizations for early modular FTQC systems.
The multi-controlled Toffoli (MCT) gate is a fundamental primitive in quantum circuit design, with applications in quantum arithmetic, cryptanalysis, and algorithmic implementations. Being a high-level logical operation, the efficient decomposition of MCT gates into lower-level netlists has remained a major optimization challenge for decades. While emerging quantum error-correcting codes such as bivariate bicycle (BB) codes drastically reduce fault-tolerance overhead, realizing non-Clifford circuits on modular BB-code architectures introduces complex compilation bottlenecks governed by inter-module routing, factory density, and layout. Consequently, the mapping of MCT gates onto BB-code architectures remains relatively unexplored.
In this paper, we overcome these challenges by mapping optimal-Toffoli-depth MCT decompositions (Dutta et al., PRA, 2025) onto BB-code-based fault-tolerant architectures via direct ∣CCZ⟩ state injection from an external magic state factory. We introduce a targeted placement strategy that exploits the binary-tree structure of MCT decompositions to co-locate interacting subtrees. This approach reduces inter-module instruction counts by up to 16.02% compared to a naive sequential first-fit placement. We also evaluate the impact of factory placement across different topologies, demonstrating that grid-based layouts yield up to a 23.7% reduction in inter-module instructions relative to linear architectures (Yoder et al., arXiv, 2025). Finally, we validate the practical viability of our compiled circuits by analyzing aggregate execution errors and logical failure probabilities using the bicycle-ISA error estimator bicycle_numerics provided by the Qiskit community, https://github.com/qiskit-community/bicycle-architecture-compiler.
Early demonstrations of fault tolerant quantum systems have paved the way for logical-level compilation. For fault-tolerant applications to succeed, execution must finish with a low total program error rate (i.e., a low program failure rate). In this work, we study a promising candidate for future fault-tolerant architectures with low spatial overhead: the Gross code. Compilation for the Gross code entails compiling to Pauli Based Computation and then reducing the rotations and measurements to the Bicycle ISA. Depending on the configuration of modules and the placement of code modules on hardware, one can reduce the amount of resulting Bicycle instructions to produce a lower overall error rate.
We find that NISQ-based, and existing FTQC mappers are insufficient for mapping logical qubits on Gross code architectures because 1. they do not account for the two-level nature of the logical qubit mapping problem, which separates into code modules with distinct measurements, and 2. they naively account only for length two interactions, whereas Pauli-Products are up to length n, where n is the number of logical qubits in the circuit. For these reasons, we introduce a two-stage pipeline that first uses hypergraph partitioning to create in-module clusters, and then executes a priority-based algorithm to efficiently assign clusters onto hardware. We find that our mapping policy reduces the error contribution from inter-module measurements, the largest source of error in the Gross Code, by up to ∼36% in the best case, with an average reduction of ∼13%. On average, we reduce the failure rates from inter-module measurements by ∼22% with localized factory availability, and by ∼17% on grid architectures, allowing hardware developers to be less constrained in developing scalable fault tolerant systems due to software driven reductions in program failure rates.
Resource estimation is a significant challenge in evaluating fault tolerant quantum computers. Existing approaches often rely on either fixed architectural assumptions or coarse analytical models that fail to capture the interaction between hardware constraints and circuit compilation. This challenge is particularly acute for neutral atom quantum computers, where architectural features such as atom movement, measurement zones, and multi-species arrays introduce a broad design space for implementing fault tolerant computation. Addressing the need for a tighter feedback loop between hardware design and practical application development, we present a compilation-driven framework for quantum resource estimation that translates arbitrary quantum circuits into logical primitive operations with known physical resource costs. This framework allows for easily configurable hardware assumptions that enable rapid comparison of different architectural design choices. We apply our approach to two early fault tolerant quantum simulation and optimization workloads, assuming the use of the surface code, revealing several architectural trends. While the production of magic states continues to be the dominant source of overhead for these benchmarks, access to movement can save time on cultivation and important transversal gates. As problem size grows, routing and qubit movement become dominant bottlenecks, highlighting the need for movement-aware compiler optimizations and frugal routing strategies. Finally, our results suggest that neutral atom architectures combining dual-species arrays with controlled qubit movement offer a promising path toward near-term advantage on fault tolerant devices.
We present the bicycle architecture, a modular quantum computing framework based on high-rate, low-overhead quantum LDPC codes identified in prior work. For two specific bivariate bicycle codes with distances 12 and 18, we construct explicit fault-tolerant logical instruction sets and estimate the logical error rate of the instructions under circuit noise. We develop a compilation strategy adapted to the constraints of the bicycle architecture, enabling large-scale universal quantum circuit execution. Integrating these components, we perform end-to-end resource estimates demonstrating that an order of magnitude larger logical circuits can be implemented with a given number of physical qubits on the bicycle architecture than on surface code architectures. We anticipate further improvements through advances in code constructions, circuit designs, and compilation techniques.
Near-term FTQC system designs are constrained by limited error budgets and largely sequential execution of non-Clifford gates. As a result, reducing the number of the most-error prone instructions becomes critical for successful program execution. In this work, we study the extractor architecture, a recently proposed FTQC design that enables universal quantum computation on spatially-efficient QEC codes such as the BB code family. In these architectures, over 90% of the total program error arises from the synthillation process, which involves ∣T⟩-state preparation and injection to implement non-Clifford gates. We observe that standard Rz synthillation requires multiple sequential ∣T⟩-state injections, each incurring an inter-module measurements, the most expensive instruction in the architecture, which cumulatively dominate the overall error budget.
To address this bottleneck, we propose INJEQT, a 2-factory design that uses an auxiliary code capable of synthesizing Rz(θ) states with lower error rates. These states are then injected into the extractor modules using only a constant number of inter-module measurements. This approach reduces overall error rates by up to 22×. We further reduce the time overhead by a pre-fetching strategy that prepares the Rz states and their correction states in parallel. This approach improves the wall-clock time by up to 13× and reduces the space-time cost by up to 7.2×, for an optimal choice of the number of INJEQT factories for each metric. We evaluate INJEQT for multiple state preparation techniques such as distillation, cultivation and STAR, and model the execution times for both lattice surgery-based and transversal CNOT based injections. Our results demonstrate that INJEQT is robust across factory choices and device technologies, enabling more efficient architectural designs for FTQC.
Quantum Error Correction (QEC) codes form the foundation of Fault-Tolerant Quantum Computing (FTQC) and predominantly use the Clifford+T gate set. Recently, Clifford operations have become the key performance bottleneck in implementing QEC. While state-of-the-art approaches like Pauli-Based Compilation (PBC) reduce Clifford overhead by transforming Clifford gates into Pauli measurements, they do so at the cost of gate-level parallelism, inflating circuit depth and execution times. To overcome these limitations, we introduce TACO, a Transpiler-Architecture Co-design framework that tackles the Clifford bottleneck through circuit and architectural optimization. TACO uses FTQC insights to guide hardware-aware Clifford gate elimination and circuit restructuring, and leverages the resulting optimized circuits to refine architectural design. TACO applies FTQC-specific transformations to aggressively reduce Clifford overhead from rotation synthesis and Toffoli decompositions, while preserving gate-level parallelism. The resulting architecture is optimized for the locality and data-movement patterns of these circuits, enabling high-throughput, resource-efficient execution. Our evaluation across diverse benchmarks shows that TACO achieves up to 21.9x (mean 4.4x) reduction in execution time compared to the state-of-the-art baseline.