As the size and complexity of a quantum computer increases, quantum bit (qubit) characterization and gate optimization become complex and time-consuming tasks. Current calibration techniques require complicated and verbose measurements to tune up qubits and gates, which cannot easily expand to the large-scale quantum systems. We develop a concise and automatic calibration protocol to characterize qubits and optimize gates using QubiC, which is an open source FPGA (field-programmable gate array) based control and measurement system for superconducting quantum information processors. We propose mutli-dimensional loss-based optimization of single-qubit gates and full XY-plane measurement method for the two-qubit CNOT gate calibration. We demonstrate the QubiC automatic calibration protocols are capable of delivering high-fidelity gates on the state-of-the-art transmon-type processor operating at the Advanced Quantum Testbed at Lawrence Berkeley National Laboratory. The single-qubit and two-qubit Clifford gate infidelities measured by randomized benchmarking are of $4.9(1.1) times 10^{-4}$ and $1.4(3) times 10^{-2}$, respectively.
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