The optimal design of a fault-tolerant quantum computer involves finding an appropriate balance between the burden of large-scale integration of noisy components and the load of improving the reliability of hardware technology. This balance can be evaluated by quantitatively modeling the execution of quantum logic operations on a realistic quantum hardware containing limited computational resources. In this work, we report a complete performance simulation software tool capable of (1) searching the hardware design space by varying resource architecture and technology parameters, (2) synthesizing and scheduling fault-tolerant quantum algorithm within the hardware constraints, (3) quantifying the performance metrics such as the execution time and the failure probability of the algorithm, and (4) analyzing the breakdown of these metrics to highlight the performance bottlenecks and visualizing resource utilization to evaluate the adequacy of the chosen design. Using this tool we investigate a vast design space for implementing key building blocks of Shor's algorithm to factor a 1,024-bit number with a baseline budget of 1.5 million qubits. We show that a trapped-ion quantum computer designed with twice as many qubits and one-tenth of the baseline infidelity of the communication channel can factor a 2,048-bit integer in less than five months.A:2 M. Ahsan et al. QUANTUM CIRCUITS Universal Quantum GatesQuantum circuits consist of a sequence of gates on qubit operands. An n-qubit quantum gate perform a deterministic unitary transformation on n operand qubits. In the termi-

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