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Temperature-aware computing is becoming more important in design of computer systems as power densities are increasing and the implications of high operating temperatures result in higher failure rates of components and increased demand for cooling capability. Computer architects and system software designers need to understand the thermal consequences of their proposals, and develop techniques to lower operating temperatures to reduce both transient and permanent component failures. Recognizing the need for thermal modeling tools to support those researches, there has been work on modeling temperatures of processors at the micro-architectural level which can be easily understood and employed by computer architects for processor designs. However, there is a dearth of such tools in the academic/research community for undertaking architectural/systems studies beyond a processor - a server box, rack or even a machine room. In this paper we presents a detailed 3-dimensional computational fluid dynamics based thermal modeling tool, called ThermoStat, for rack-mounted server systems. We conduct several experiments with this tool to show how different load conditions affect the thermal profile, and also illustrate how this tool can help design dynamic thermal management techniques. We propose reactive and proactive thermal management for rack mounted server and isothermal workload distribution for rack.