In the era of cloud computing, data centers that accommodate a series of user-requested jobs with a diversity of resource usage pattern need to have the capability of efficiently distributing resources to each user job, based on individual resource usage patterns. In particular, for high-performance computing as a cloud service which allows many users to benefit from a large-scale computing system, a new framework for resource management that treats not only the CPU resources, but also the network resources in the data center is essential. In this paper, an SDN-enhanced JMS that efficiently handles both network and CPU resources and as a result accelerates the execution time of user jobs is introduced as a building block technology for such a HPC cloud. Our evaluation shows that the SDN-enhanced JMS efficiently leverages the fat-tree interconnect of cluster systems running behind the cloud to suppress the collision of communications generated by different jobs.