Container-based virtualization represents a flexible and scalable solution for HPC environments, allowing a simple and efficient management of scientific applications. Recently, Systems-on-a-Chip (SoC) have emerged as an alternative to traditional HPC clusters, with a good computing power and low costs. In this paper, we present how we developed a container-based solution for SoC clusters, and study the performance of WRF (Weather Research and Forecasting) in such environments. The results demonstrate that although the peak performance of SoC clusters is still limited, these environments are more than suitable to scientific application that have relaxed QoS constraints.