Nowadays, the trend of developing micro-processor with tens of cores brings a promising prospect for embedded systems. Realizing a high performance and low power many-core processor is becoming a primary technical challenge. We are currently developing a many-core processor architecture for embedded systems as a part of a NEDO's project. This paper introduces the many-core architecture called SMYLEref along whit the concept of Virtual Accelerator on Many-core, in which many cores on a chip are utilized as a hardware platform for realizing multiple virtual accelerators. We are developing its prototype system with off-the-shelf FPGA evaluation boards. In this paper, we introduce the architecture of SMYLEref and the detail of the prototype system. In addition, several initial experiments with the prototype system are also presented.