A method of performing a quantum computation process includes mapping, by a classical computer, logical qubits to physical qubits of a quantum processor so that quantum circuits are executable using the physical qubits of the quantum processor and a total infidelity of the plurality of quantum circuits is minimized, wherein each of the physical qubits comprise a trapped ion, and each of the plurality of quantum circuits comprises single-qubit gates and two-qubit gates within the plurality of the logical qubits, calibrating, by a system controller, two-qubit gates within a first plurality of pairs of physical qubits, such that infidelity of the two-qubit gates within the first plurality of pairs of physical qubit is lowered, executing the plurality of quantum circuits on the quantum processor, by applying laser pulses that each cause a single-qubit gate operation and a two-qubit gate operation in each of the plurality of quantum circuits on the plurality of physical qubits, measuring, by the system controller, population of qubit states of the physical qubits in the quantum processor after executing the plurality of quantum circuits on the quantum processor, and outputting, by the classical computer, the measured population of qubit states of the physical qubits as a result of the execution the plurality quantum circuits, wherein the result of the execution the plurality quantum circuits are configured to be displayed on a user interface, stored in a memory of the classical computer, or transferred to another computational device.