Clusters based on open-source software and the Linux operating system have come to dominate high performance computing (HPC). This is due in part to their superior performance, cost-effectiveness and flexibility. The same factors that make open-source software the choice of HPC professionals have also made it less accessible to smaller centers. The complexity and associated cost of deploying and managing open-source clusters threatens to erode the very cost benefits that have made them compelling in the first place. As customers choose between open-source and commercial alternatives, there are many different costs related to administration and productivity that should be considered. These are explored in this paper in order to give a true cost perspective. We also examine how a commercial management product, such as IBM Platform HPC, enables HPC customers to side-step many overhead cost and support issues that often plague open-source environments and enable them to deploy powerful, easy to use clusters. The hidden costs of open source