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FishEye and Crucible are separate products. They can be run separately, and they can also be run together.
You can run Crucible standalone, but you will not have access to some of FishEye's advanced features, such as pre-caching repository content (for maximum performance), advanced searching and FishEye's activity graphs.
Crucible stand-alone can be used with Subversion, CVS, Perforce, Git and Clearcase via SCM plugins. In this situation, access to the repositories is strictly on-demand.
For the best combination of features and performance, run both Crucible and FishEye.