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The emergence of e-science provides new research methods and modes and brings scientific research into information's new era: scientists use kinds of resources located in different areas to complete their computing applications, such as scientific computing model, scientific data and computing clusters. Although this new mode has already brought many benefits, it makes people who involve in this process have to face many new problems and challenges. This paper discusses the problems and challenges scientific computing facing in distributed environment in detail; and on this discussion's results, we propose SMAIA- a semantic model-based automatic integrated architecture for scientific computing application - to meet needs in scientific computing completely, and SMAIA is also flexible and scalable. The main contribution of this paper is that the semantic based scientific computing application model and resource description, which are the core of SMAIA. Finally, we apply SMAIA in earthquake computing domain to demonstrate its capabilities.