High Performance Computing (HPC) systems mainly focused on how to improve performances of the computing. It has competitive processing capacity both in terms of calculation speed and available memory. HPC infrastructures are valuable computing resources that need to be carefully guarded and avoid being maliciously used. Thus, vulnerabilities are quintessential issues in HPC systems due to most of jobs and resources run or stored usually are sensitive and high-profit information. In this survey, we comprehensively review securities of HPC systems from a log-analyzing perspective, including well-known attacks and widely used defenses, especially intruder detection methods. We found that log files are used for the security purposes much less than what we expected. How to use all the available log files comprehensively and employ state-ofthe-art intrusion techniques to improve the robustness of HPC systems still lies for future research.