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Fixed-point iteration over parallel relational algebra (RA) operators underpins a broad class of symbolic AI and recursive analytic workloads, including graph reachability, points-to analysis, and rule-based inference. At scale, each iteration materializes substantial intermediate and output relations across distributed memory, causing persistence I/O to become a dominant contributor to end-to-end cost. This I/O is inherently write-dominated: every iteration emits a delta of newly derived tuples, while the runtime must periodically checkpoint accumulated relation state to stable storage for fault tolerance and out-of-core execution. This paper presents a case study in optimizing checkpoints for parallel iterated relational algebra, comparing an existing relation-dumping pipeline against a structured, performance-tuned alternative. The baseline stores relations as opaque binary dumps via POSIX positioned writes or collective MPIIO with minimal file-system hinting.We extend this pipeline with a parallel HDF5 backend that stores relations as schema-aware datasets and writes rank partitions using HDF5 hyperslabs with collective transfers. To avoid the performance cliffs associated with default parallel HDF5 settings, we apply a systematic size-aware tuning policy that configures both HDF5 property lists and MPI-IO hints. The optimized pathway uses a two-phase workflow that creates the file and dataset first and then performs the parallel write. It also applies output-regime-dependent alignment and buffering, configures metadata caching and sieve buffering, selects an appropriate dataset layout, and enforces collective dataset transfers. Across final write sizes from 15 GB to 30 GB, the tuned HDF5 path consistently outperforms the MPI-IO baselines. At higher MPI process counts, it is often 35%-58% faster while producing self-describing outputs.