A number of parallel applications run on a high-performance computing (HPC) system simultaneously. Job mapping and scheduling become crucial to improve system utilization, because fragmentation prevents an incoming job from being assigned even if there are enough compute nodes unused. Wireless supercomputers and datacenters with free-space optical (FSO) terminals have been proposed to replace the conventional wired interconnection so that a diverse application workload can be better supported by changing their network topologies. In this study we firstly present an efficient job mapping by swapping the endpoints of FSO links in a wireless HPC system. Our evaluation shows that an FSO-equipped wireless HPC system can achieve shorter average queuing length and queuing time for all the dispatched user jobs. Secondly, we consider the use of a more complicated and enhanced scheduling algorithm, which can further improve the system utilization over different host networks, as well as the average response time for all the dispatched user jobs. Finally, we present the performance advantages of the proposed wireless HPC system under more practical assumptions such as different cabinet capacities and diverse subtopology packings.