A quantum computing system includes a quantum processor having a plurality of qubits, a classical memory, and a classical processor. The classical processor is configured to compile a quantum program into logical assembly instructions in an intermediate language, aggregate the logical assembly instructions together into a plurality of logical blocks of instructions, generate a logical schedule for the quantum program based on commutativity between the plurality of logical blocks, generate a tentative physical schedule based on the logical schedule, the tentative physical schedule includes a mapping of the logical assembly instructions in the logical schedule onto the plurality of qubits of the quantum processor, aggregate instructions together within the tentative physical schedule that do not reduce parallelism, thereby generating an updated physical schedule; generate optimized control pulses for the aggregated instructions, and execute the quantum program on the quantum processor with the optimized control pulses and the updated physical schedule.