The use of virtualization technologies in high performance computing (HPC) environments has traditionally been avoided due to their inherent performance overhead. However, with the rise of container-based virtualization implementations, such as Linux VServer, OpenVZ and Linux Containers (LXC), it is possible to obtain a very low overhead leading to near-native performance. In this work, we conducted a number of experiments in order to perform an in-depth performance evaluation of container-based virtualization for HPC. We also evaluated the trade-off between performance and isolation in container-based virtualization systems and compared them with Xen, which is a representative of the traditional hypervisor-based virtualization systems used today.