Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs’ high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Integrating recent advancements in resilient algorithms and techniques into existing codes is a singular challenge in fault tolerance - in part due to the underlying complexity of implementing resilience in the first place, but also due to the difficulty introduced when integrating the functionality of a standalone new strategy with the preexisting resilience layers of an application. We propose that the answer is not to build integrated solutions for users, but runtimes designed to integrate into a larger comprehensive resilience system and thereby enable the necessary jump to multi-layered recovery. Our work designs, implements, and verifies one such comprehensive system of runtimes. Utilizing Fenix, a process resilience tool with integration into preexisting resilience systems as a design priority, we update Kokkos Resilience and the use pattern of VeloC to support application-level integration of resilience runtimes. Our work shows that designing integrable systems rather than integrated systems allows for user-designed optimization and upgrading of resilience techniques while maintaining the simplicity and performance of all-in-one resilience solutions. More application-specific choice in resilience strategies allows for better long-term flexibility, performance, and - importantly - simplicity.