This commit improves memory management by respecting Linux cgroup v1/v2 limits and introduces a configurable memory budget for the new `rebuild` subcommand to prevent OOM during index reconstruction. The rebuild process now supports filtering, compaction, and parallelization. Diagnostic capabilities are expanded with debug-level tracing for partition merges, k-mer expansion tracking, and utility flags for label renaming, matrix size breakdowns, per-genome counts, and partition distribution reporting. Accessor methods for active and remaining memory have also been added to the stats struct.
Introduces a memory-aware scheduling strategy for parallel partition merging that replaces unbounded concurrency with a First-Fit Decreasing approach gated by a thread-safe `MemoryBudget` semaphore. An adaptive expansion factor, seeded by a sequential pilot run, dynamically caps concurrent workers to prevent hashbrown OOMs. Adds a `--budget-fraction` CLI flag to configure RAM allocation, enhances the CLI to accept multiple indexes, and introduces comprehensive partition diagnostics including memory utilization tracking, concurrency metrics, and statistical summaries with ASCII histograms. Updates documentation and navigation accordingly.
Add the `tracing` crate to `obidebruinj`, `obisys`, and resolve it in `Cargo.lock`. Replace `eprintln!` statements with structured `debug!` and `info!` macros. Introduce a `TracedBar` wrapper for progress bars and enhance the `Stage` lifecycle to emit structured events for timing, memory metrics, and swap warnings. Add a progress spinner for unitig degree computation. Extend `PersistentBitMatrix` with columnar bit-vector operations and parallel distance methods, enabling uniform distance computations across all storage layouts while replacing previous panics with dimension-based fallbacks.
This commit introduces the `obisys` crate, which wraps `indicatif` to provide reusable `spinner` and `progress_bar` utilities with consistent styling and tick intervals. It refactors progress reporting across `obikindex`, `obikpartitionner`, and `obikmer` to use these shared functions, eliminating inline UI configuration and ensuring uniform terminal feedback.
Introduce zero-allocation row extraction and query result buffers across `obicompactvec` and `obikpartitionner` to eliminate per-kmer heap allocations. Replace in-memory MPHF deserialization with memory-mapped, zero-copy views to reduce runtime memory footprint. Add configurable I/O chunking, a RAM-aware `--chunk-size` parameter, and system memory monitoring via the new `sysinfo` dependency. Re-export `PreloadedIndex` for external consumers.
The previous `major_faults > 10` check is unreliable on macOS, as it counts file-backed mmap page-ins rather than true memory pressure. This change replaces it with `swaps > 0`, a more accurate cross-platform indicator of RAM exhaustion. The swap diagnosis message is also updated to clarify that the working set exceeds available RAM, and comments are added to document this rationale.
Establishes the `obisys` crate using Rust 2024 and the `libc` dependency. Introduces a lightweight profiler that captures wall-clock time and `getrusage` system metrics per pipeline stage. Automatically computes parallelism and efficiency ratios, detects bottlenecks such as memory pressure and disk I/O, and prints a formatted diagnostic summary to stderr.
Eric Coissac