The performance of modern mainframe computers keeps increasing due to the advances in the semiconductor technology. However, the quest for the faster computer has never been satisfied. To overcome the discrepancy in the supply and demand, we studied a high performance computer architecture utilizing a three-dimensional Holographic Data Storage Systems (HDSS) as a secondary storage system. The HDSS can achieve a high storage density by utilizing the third dimension. Furthermore, the HDSS can exploit the parallelism by processing the two-dimensional data in a single step. To compare the performance of the HDSS with the conventional hard disk based storage system, we modeled the HDSS using the DiskSim simulation engine and performed the simulation study. Results showed that the HDSS can improve the access time by 1.7 times.