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Graphics Processing Units (GPUs) are increasingly used to solve non-graphical scientific problems. However, it has been shown that the reliability of the GPUs is a concern because of the occurrence of the soft and hard errors. The checkpoint/restart is the most commonly used technique to achieve fault tolerance in the presence of failures. This work present an application-level checkpoint scheme for systems composed of GPUs. Our scheme exploits the benefits of the divide-and-conquer technique and of the communication-computation overlapping to improve the execution time and checkpoint overhead. By dividing the problem and checkpointing in n subprocesses, we show that our scheme improves the checkpoint overhead by a factor of n. We also show that dividing the problem with finer granularity is not beneficial.