Different departments of a large organization often run dedicated cluster systems for different computing loads, like HPC (high performance computing) jobs or Web service applications. In this paper, we have designed and implemented a cloud management system software Phoenix Cloud to consolidate heterogeneous workloads from different departments affiliated to the same organization on the shared cluster system. We have also proposed cooperative resource provisioning and management policies for a large organization and its affiliated departments, running HPC jobs and Web service applications, to share the consolidated cluster system. The experiments show that in comparison with the case that each department operates its dedicated cluster system, Phoenix Cloud significantly decreases the scale of the required cluster system for a large organization, improves the benefit of the scientific computing department, and at the same time provisions enough resources to the other department running Web services with varying loads.