Optimizing Write Performance for Checkpointing to Parallel File Systems Using LSM-Trees

The widening gap between compute performance and I/O performance on modern HPC systems means that writing checkpoints to a parallel file system for fault tolerance is fast becoming a bottleneck to high-performance. It is therefore vital that software is engineered such that it can achieve the highest proportion of available performance on the underlying hardware; and this is a burden often carried by I/O middleware libraries. In this paper, we outline such an I/O library based on a Log-structured Merge Tree (LSM-Tree), not just for metadata, but also scientific data. We benchmark its performance using the IOR benchmark, demonstrating 2.4 to 76.7x better performance than alternative file formats, such as ADIOS2, HDF5, and IOR baseline when running on a Lustre Parallel File System. We further demonstrate that when our LSM-Tree I/O library is used as a storage layer for ADIOS2, the resulting I/O library still outperforms the default ADIOS2 implementation by 1.5x.