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Cloud computing is a new trend of computer science and technology. Cloud computing may become a major tool for researchers to access processors and storage. Cloud computing brings both opportunities and challenges to high performance computing (HPC). Infinite on-demand computing resource can make HPC much more convenient and common than ever before. However, the virtualization paradigm which has been widely used in the cloud computing systems will decrease the running efficiency of the physic machine. We described some difficulties to implement high performance computing of finite element analysis in the cloud computing systems, and gave some candidate solutions in this article.