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Nowadays, more and more scientific applications are moving to cloud computing. The optimal deployment of scientific applications is critical for providing good services to users. Scientific applications are usually topology-aware applications. Therefore, considering the topology of a scientific application during the development will benefit the performance of the application. However, it is challenging to automatically discover and make use of the communication pattern of a scientific application while deploying the application on cloud. To attack this challenge, in this paper, we propose a framework to discover the communication topology of a scientific application by pre-execution and multi-scale graph clustering, based on which the deployment can be optimized. Comprehensive experiments are conducted by employing a well-known MPI benchmark and comparing the performance of our method with those of other methods. The experimental results show the effectiveness of our topology-aware deployment method.