This paper investigates the performance degradation in application programs running on virtual machines (VMs) in a physical computing server with a focus on HPC applications. We select three benchmarks as the expected workload in a data center: HPC applications, database applications, and web server applications. Then, we put VMs executing two application programs together in a physical computing server and evaluate the performance degradation in each application program. We also investigate the resource consumption in each application program and the reason for the performance degradation. The experimental results indicate that the interference among VMs executing two HPC application programs with high memory usage and high network I/O in the physical computing server significantly degrades the application performance.