Code coupling applications can be divided into communicating modules, that may be executed on different clusters in a cluster federation. As a cluster federation comprises of a large number of nodes, there is a high probability of a node failure. We propose a hierarchical checkpointing protocol that combines a synchronized checkpointing technique inside clusters and a communication-induced technique between clusters. This protocol fits to the characteristics of a cluster federation (large number of nodes, high latency and low bandwidth networking technologies between clusters). A preliminary performance evaluation performed using a discrete event simulator shows that the protocol is suitable for code coupling applications.