Rockhopper, a true HPC system built with cloud concepts

A number of services for scientific computing based on cloud resources have recently drawn significant attention in both research and infrastructure provider communities. Most cloud resources currently available lack true high performance characteristics, such as high-speed interconnects or storage. Researchers studying cloud systems have pointed out that many cloud services do not provide service level agreements that may meet the needs of the research community. Furthermore, the lack of location information provided to the user and the shared nature of the systems use may create risk for users of the system, in the instance that their data is moved to an unknown location with an unknown level of security. Indiana University and Penguin Computing have partnered to create a system, Rockhopper, which addresses many of these issues. This system is a true high performance resource, with on-demand allocations, control, and tracking of jobs, situated at Indiana University´s high-security datacenter facility. Rockhopper allows researchers to flexibly conduct their work under a number of use cases while also serving as an extension of cyberinfrastructure that scales from the researcher´s local environment all the way up through large national resources. We describe the architecture and ideas behind the creation of the system, present a use case for campus bridging, and provide a typical example of system usage. In a comparison of Rockhopper to a cloud-based system, we run the Trinity RNA-seq software against a number of datasets on both the Rockhopper system and on Amazon´s EC2 service.