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High-Performance Computing (HPC) in the cloud has reached the mainstream and is currently a hot topic in the research community and the industry. The attractiveness of cloud for HPC is the capability to run large applications on powerful, scalable hardware without needing to actually own or maintain this hardware. In this paper, we conduct a detailed comparison of HPC applications running on three cloud providers, Amazon EC2, Microsoft Azure and Rackspace. We analyze three important characteristics of HPC, deployment facilities, performance and cost efficiency and compare them to a cluster of machines. For the experiments, we used the well-known NAS parallel benchmarks as an example of general scientific HPC applications to examine the computational and communication performance. Our results show that HPC applications can run efficiently on the cloud. However, care must be taken when choosing the provider, as the differences between them are large. The best cloud provider depends on the type and behavior of the application, as well as the intended usage scenario. Furthermore, our results show that HPC in the cloud can have a higher performance and cost efficiency than a traditional cluster, up to 27% and 41%, respectively.