A computing system includes a quantum processor with qubits, a classical memory including a quantum program defining a plurality of instructions in a source language, and a classical processor configured to: (i) receive a circuit of gates representing a quantum program for a variational algorithm in which computation is interleaved with compilation; (ii) identify a plurality of blocks, each block includes a subcircuit of gates, leaving one or more remainder subcircuits of the circuit of gates outside of the plurality of blocks; (iii) pre-compile each block of the plurality of blocks with a pulse generation program to generate a plurality of pre-compiled blocks including control pulses configured to perform the associated block on the quantum processor; and (iv) iteratively execute the quantum program using the pre-compiled blocks as static during runtime and recompiling the one or more remainder subcircuits on the classical processor at each iteration of execution.