Wenjie Sun, Xiaoyu Li, Zhigang Wang, Geng Chen, Lianhui Yu, Guowu Yang

As quantum computing advances towards practical applications, quantum operating systems become inevitable, where multi-programming -- the core functionality of operating systems -- enables concurrent execution of multiple quantum programs to enhance hardware utilization. However, most quantum compilation work focuses solely on single-circuit execution, severely limiting resource efficiency and hindering quantum operating system development. We propose Dynamic Neutral Atom Multi-programming Optimizer (DYNAMO), a method that realizes multi-programming on neutral atom quantum architectures through parallel compilation and intelligent resource allocation across multiple quantum processing units (QPUs). DYNAMO addresses two critical challenges: inefficient and difficult resource partitioning, and complex scheduling conflicts from concurrent program. Our method enables efficient spatial and temporal resource sharing while maintaining circuit correctness and hardware constraints. Experimental evaluation across circuits ranging from 12 to over 1200 gates demonstrates that DYNAMO achieves up to 14.39x compilation speedup while reducing execution stages by an average of 50.47%. Furthermore, DYNAMO successfully distributes workloads across multiple QPUs with balanced resource utilization. By enabling efficient multi-programming capabilities, DYNAMO establishes a critical foundation towards realizing practical quantum operating systems.