We present a network configuration scheme exampled by a hardwired 64-node parallel computer with interconnection topologies of 2D Torus(8 x 8), 2D iBT(8 x 8; b = 〈2〉) and 3D Torus(4 x 4 x 4) reconfigurated by software. On this platform, we evaluate the performance ratios through adding bypass links (iBT) or torus links (3D Torus) to the base 2D Torus. We benchmark the three network topologies on elementary and collective communications as well as parallel applications including NAS parallel benchmark, NAMD, high performance Linpack and HPC challenge benchmark suites. Through comparative analysis of the relative performances, we reveal and, in several cases, reaffirm that strategically adding links could greatly improve the performance in 94 percent tested application cases; the iBT network outperforms others in more than half of the tested cases; and our network configuration scheme would be an alternative, better than the classical network scheme, for constructing a parallel processing system with a variety of application patterns.