Iris recognition has become a widely popular biometric system. The stable textures and features of the human iris have made such biometric systems efficient and accurate for purposes of verification and identification. The term non-ideal iris refers to a situation in which the iris is occluded by noise, including reflections, eyelashes, eyelids and so on. Most current iris recognition algorithms assume that the iris is not occluded, which is less accurate. A method using only some parts of the iris may be suitable to deal with a non-ideal iris. The current application of iris recognition systems are plagued by weaknesses such as slow processing times, especially when dealing with many irises. In this study, a sub-iris recognition technique is proposed to deal with the non-ideal iris, while reducing execution time via an embedded system using a graphical processing unit (GPU). The experiment revealed that the proposed method was accurate and fast.