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Virtualizing complex hardware, such as heterogeneous multiprocessor systems, enables developers to use standard Application Programming Interfaces (APIs) for application integration. Especially, the supply of an Operating System (OS) is well appreciated since many features such as drivers, the runtime environment and scheduling mechanisms are available and well established. For this purpose, Embedded Linux was used as basis OS and extended in order to be able to manage a Runtime Adaptive Multi-Processor System-on-Chip (RAMPSoC) and to provide the standard Message Passing Interface (MPI). This paper describes the adaptation of the Linux kernel supporting MPI with runtime libraries as well as the integration of the software/hardware drivers which supply the message transfer over a reconfigurable and heterogeneous Network-on-Chip (NoC).