obikmer/DevDocMD/implementation/partition_layer_cache.md

Partition and layer caching (discussion)

Status: problem confirmed, design direction agreed (2026-08-20). (1)/(2) themselves not started; ownership split (below) still open. Preparatory encapsulation work (partition/layer path and metadata accessors on KmerPartition) landed the same day — see "Preparatory work done" below.

Type-to-concept mapping: Index / Partition / Layer

The conceptual nesting Index { Partition { Layer { MPHF, Evidence, Matrix } } } } does not have one Rust type per level — worth stating explicitly, since two of the names below are misleading.

• Index = obikindex::KmerIndex — { root_path, meta: IndexMeta, partition: KmerPartition }. The field is named partition (singular), but it holds the whole multi-partition structure below — the name suggests "one partition", the value is all of them.
• Partition, the collection (not one partition) = obikpartition::KmerPartition. Despite the singular name, this owns every partition of the index: root_path, n_partitions, and per-partition accessors that all take an explicit index i (partition_dir(i), index_dir(i), layer_dir(i, l), partition_meta(i), n_layers(i), index_mode(i) — see the part_dir/layer_dir and PartitionMeta-encapsulation work above). It never holds one partition's layers open in memory — no Vec<Layer<D>> here, only path arithmetic and metadata reads. A more honest name would be KmerPartitionSet or KmerPartitioner; renaming is out of scope for now, just worth knowing it's not "a partition."
• Partition, one of them = no dedicated type exists today. The structural equivalent of "one partition, its layers held open" is obilayeredmap::LayeredMap<D> — { root, meta: PartitionMeta, layers: Vec<Layer<D>> } — but LayeredMap itself doesn't know it's playing that role: it operates purely on whatever root path it's given and has no notion of KmerPartition, n_partitions, or a partition index i (see "Layering: who owns what" below — established independently while fixing open_data/layer_dir). Every caller that wants "one partition, opened" builds the path itself (kmer_partition.index_dir(i)/.layer_dir(i, l)) and either passes it to LayeredMap::open or — as obikphylo::siblings::cache does — bypasses LayeredMap entirely and opens each Layer<D> directly.
• Layer = obilayeredmap::Layer<D> — { mphf: MphfLayer, data: D }.
  • MPHF = MphfLayer.mphf: MemCase<MphfEps> — kmer → slot.
  • Evidence = MphfLayer.ev: LayerEvidence (Exact/Approx/ Hybrid — evidence.bin/fingerprint.bin; see EvidenceKind).
  • Matrix = Layer<D>.data: D — PersistentBitMatrix / PersistentCompactIntMatrix / PersistentSparseBitMatrix / ().

Today's actual nesting, in Rust terms:

KmerIndex
 └─ partition: KmerPartition                 (all N partitions — paths + metadata only)
     └─ (opened on demand, per i)  LayeredMap<D>   ← "one partition", unnamed as such
         └─ layers: Vec<Layer<D>>
             └─ Layer<D> { mphf: MphfLayer, data: D }
                 ├─ mphf.mphf   → MPHF
                 ├─ mphf.ev     → Evidence
                 └─ data        → Matrix

obikphylo::siblings::cache::PartitionCache — the thing (2) is meant to generalise — skips the middle of this nesting entirely: it doesn't build a Vec<LayeredMap<D>>, it builds mats: Vec<Vec<Mat>> directly — outer index = partition i (via KmerPartition), inner index = layer l (via Layer<D>/Mat) — reconstructing "one partition, its layers open" as a bare nested Vec because no owning type for that concept exists to reuse. That gap is exactly what (2) needs to fill, and (1) is exactly what would let a per-partition type hold layers of mixed D (today LayeredMap<D> can't, being monomorphic — see "The gap in obilayeredmap's existing cache" below).

Major restructuring (2026-08-20): KmerPartitions merged into KmerIndex

Prompted by a direct question: why keep KmerIndex/KmerPartitions split when, one level down, KmerPartitions is going to directly hold Vec<KmerPartition> rather than being split again into "collection-holder" + "collection"? Investigating the actual justification ("KmerPartitions has an independent lifecycle, used before an index exists") turned out to be false — KmerPartitions::create was called in exactly one place, inside KmerIndex::create, and every open_with_config reopen outside KmerIndex's own constructors was a redundant re-derivation of a KmerPartitions already reachable via index.partition() (the exact kind of duplication this whole doc has been tracking). Once that was gone, so was the reason to keep them separate.

Second correction, from the same conversation: obikpartitionner had accumulated query/merge/select/rebuild/dump/distance logic that has nothing to do with partitioning super-kmers — it operates on layers, which don't exist yet at the phase obikpartitionner is actually responsible for (scatter → dereplicate → count, all pre-layer). That logic moved to obikindex, which already depends on obilayeredmap and never needed obikpartitionner for it. No crate-dependency inversion was needed — obikindex → obikpartitionner stays the same direction as before.

Result:

• obikpartitionner (renamed back from obikpartition) now contains only PartitionRouter (superkmer routing: write/write_batch/flush/ close, dereplicate, count_kmer, KmerSpectrum) and the partition_dir(root, i) naming primitive both PartitionRouter and KmerIndex build on. KmerPartitions no longer exists as a type.
• KmerIndex (obikindex) absorbed KmerPartitions's read-side entirely: partition_dir/index_dir/layer_dir/partition_meta/n_layers/ partition_mode/n_partitions (the last now derived from 2^config.n_bits, no longer a stored, independently-set duplicate field — kmer_size/minimizer_size used to be double-stored, in both KmerPartitions and IndexMeta.config, a latent-drift risk flagged earlier in this doc; now single-sourced from IndexMeta.config). Seven whole files moved from obikpartitionner into obikindex verbatim as impl KmerIndex blocks, kept as separate files (not merged into existing same-topic files): index_layer.rs, query_layer.rs, merge_layer/, select_layer.rs, rebuild_layer.rs, dump_layer.rs, plus distance.rs's count_store/presence_store (renamed matrix_store.rs to avoid colliding with obikindex's own pre-existing distance.rs), and their shared support (common.rs's load_meta/ olm_to_sk, filter.rs, graph_pipeline.rs).
• obikphylo::siblings::cache::PartitionCache::build now takes &KmerIndex directly instead of a separately-opened &KmerPartitions — this deleted the redundant-reopen pattern at all 8 call sites (alignment/build/cardinality/distance/entropy×2/ sankoff_bundle/stats), the same bug flagged earlier in this conversation as a side effect of investigating the false "independent lifecycle" claim.
• KmerIndex::partition()/partition_mut() are gone; scatter() (obikmer) and any write-side code get a transient PartitionRouter via KmerIndex::partition_router().
• A real bug caught by the test suite during this move: PartitionRouter::open initially defaulted to closed: true (inherited from KmerPartitions::open_with_config's old read-only-reopen semantics), which broke every write through a router obtained via partition_router(). Fixed — PartitionRouter is exclusively a write/processing tool now, so open always starts open.

Full workspace test suite green (0 failed) after, including all 27 obikphylo::siblings tests.

(1) done (2026-08-20): Layer is now the heterogeneous handle, Mat is gone

Resolved the naming question left open above. Layer<D> (the old generic/monomorphic type) renamed to TypedLayer<D> throughout (obilayeredmap, obikindex, obikphylo — 12 files, mechanical) to free Layer for the type that's actually meant to be everyone's default handle. obilayeredmap::content_layer::Layer (re-exported at the crate root) is that type — Count(TypedLayer<PersistentCompactIntMatrix>)/ Presence(TypedLayer<PersistentBitMatrix>), Layer::open doing the same disk probe Mat::open used to, find_slot/index_batch/n_cols/ fill_sub_matrix_carries dispatching per variant exactly as Mat did.

obikphylo::siblings::cache::Mat deleted outright — PartitionCache now holds Vec<Vec<obilayeredmap::Layer>> directly. The one sibling-specific method Mat carried (iter_minorants_batch) is not on obilayeredmap:: Layer (phylo concepts don't belong in obilayeredmap) — it's an impl SiblingLayerExt for obilayeredmap::Layer in iter.rs, dispatching to each variant's existing impl<D: LayerData> SiblingLayerExt for TypedLayer<D>.

Full workspace suite green (0 failed) after, including all 27 obikphylo::siblings tests.

Still not built: (2) — KmerPartition (singular, one partition's open Vec<Layer>) and a multi-partition cache in obikpartitionner to replace obikphylo::siblings::cache::PartitionCache and obikindex::query_layer's still-separate QueryLayer (which still independently bundles MPHF+matrix, 2-way not using Layer at all). Both remaining consumers now sit one Layer::open call away from unifying onto (2) once it exists.

The problem

Reading a layer's data (MPHF + matrix) is not free: MphfLayer::open mmaps mphf.bin plus (evidence.bin/fingerprint.bin + unitigs.bin), and the matrix side mmaps matrix.pbmx/matrix.pcmx (or one file per genome column if not yet packed). Any code path that reopens a layer per lookup instead of once per run pays this cost repeatedly.

obikphylo::siblings::cache::PartitionCache was built to avoid exactly this for build_sibling_annex/sibling_annex_stats: those commands probe many partitions, once per source layer, over the whole run. Profiling a real run showed wall-clock time dominated by repeated open()/mmap syscalls, not computation — parallelising the naive per-lookup opens spread the cost across cores without reducing it. PartitionCache::build opens every partition's every layer once, up front, in parallel, and keeps the handles alive for the run.

Three independent implementations of the same bundle

Searching the codebase for "who bundles MPHF + matrix, with per-layer format auto-detection" turns up three unrelated implementations:

	lives in	scope	cached?
Layer<D>	obilayeredmap	one layer, D fixed at compile time	held alive by whoever owns the Layer, no policy of its own
Mat	obikphylo::siblings::cache	one layer, format resolved per instance from an enum of 3 Layer<D> variants	yes, via PartitionCache
QueryLayer	obikpartition::query_layer	one layer, (MphfLayer, PersistentBitMatrix|PersistentCompactIntMatrix) pair, bypasses Layer<D> entirely	no — opened fresh inside query_partition_with on every call

query_partition_with is obikmer query's normal query path — the one most exposed to repeated cross-partition lookups — and it is the one with no cache at all. obikphylo built a cache first only because sibling-annex construction hits the cost hardest, not because the need is sibling-specific.

The gap in obilayeredmap's existing cache

obilayeredmap::LayeredMap<D> already caches correctly at the granularity of one partition: open(root) opens every layer once, keeps Vec<Layer<D>> alive for the LayeredMap's lifetime. But it is monomorphic — every layer in the Vec must share the same concrete D. In practice this is false: layers in the same partition are packed independently over time (pack --sparse converts one layer's presence matrix at a time), so a partition can genuinely mix PersistentBitMatrix-backed and PersistentSparseBitMatrix-backed presence layers. LayeredMap<D> cannot represent that mix — Mat's 3-way enum exists specifically to work around this gap, one crate away from where the gap actually is.

Resource cost: mmap does not hold a file descriptor

Before deciding how many layers/partitions a cache may hold open simultaneously, the binding constraint needs to be identified correctly.

Confirmed against upstream documentation, not inferred from behaviour:

"After the mmap() call has returned, the file descriptor, fd, can be closed immediately without invalidating the mapping." — mmap(2), man7.org

"The close(2) function does not unmap pages" — mmap(2), Apple Developer

"A file backed Mmap ... will remain valid even after the File is dropped. ... the Mmap handle is completely independent of the File used to create it." — memmap2::Mmap, docs.rs

Every read-only mmap in this codebase already follows this: Mmap::map(&File::open(path)?)? — the File is a temporary, dropped (fd closed) immediately after the mapping is established; every persistent struct (PersistentBitVec, PersistentCompactIntVec, PackedBitMatrix, Evidence, FingerprintVec, ...) stores only the Mmap, never the File. So a cache built on these types does not consume the process's open-file-descriptor budget (ulimit -n, notoriously low by default on macOS) proportionally to how many mmapped files it holds.

It does consume a different resource — the process's virtual-memory mapping table (one entry per active mmap() region). Linux exposes this as vm.max_map_count (default 65530). No documented macOS equivalent (fixed numeric ceiling) was found; the constraint there appears to be virtual address space rather than an explicit mapping counter, but this is not sourced and should not be assumed. This is the resource actually worth measuring before deciding on cache size, not fd count — and it is why packing (matrix.pbmx/matrix.pcmx, one mmap for all columns) matters independently of any caching decision: an unpacked Columnar matrix opens one mmap per genome column, multiplying the mapping count a cache would have to hold by n_genomes.

Layering: who owns what

Established in discussion, not yet coded:

• obilayeredmap operates within a single partition's index root; it has no notion of "partition" (confirmed independently while fixing open_data/layer_dir — see git history around 2026-08-20). One LayeredMap<D> (or its heterogeneous-D successor) = one partition.
• Nobody currently owns "the collection of partitions" as reusable state. obikpartition::KmerPartition is the closest candidate — it already owns n_partitions()/part_dir(i) — but today it is a pure config/path resolver, not a state holder: dereplicate, count_kmer, obikindex's distance.rs/stats.rs, and obikphylo::PartitionCache::build each independently write their own (0..n_partitions).into_par_iter().map(...) loop and open what they need from scratch.

Direction agreed, not yet implemented

1. A heterogeneous-format layer type in obilayeredmap (name TBD), generalising Mat's 3-way enum + auto-detection — obilayeredmap already implements LayerData for all three concrete matrix types involved, so it already has the knowledge Mat needed and had to duplicate.
2. A cache spanning multiple partitions, keeping (2)'s layer type open per partition per layer, for the whole lifetime of a long-running command — generalising PartitionCache minus its sibling-specific parts (fast_mode, find_presence_batch) — living in obikpartition (owner of the partition dimension) and built on top of (1).
3. obikpartition::query_partition_with — the normal query path, currently uncached — becomes a consumer of (2), not just obikphylo::PartitionCache.

Open before implementing: exact API shape of (1) and (2), whether Mat is deleted outright or kept as a thin sibling-specific wrapper, and whether (2) needs an eviction policy or can simply hold every partition open for the process lifetime (revisit once the VM-mapping-count question above has a real number behind it for this codebase's scale).

Preparatory work done (2026-08-20)

Groundwork for (1)/(2), landed ahead of the design itself:

• KmerPartition (obikpartition) gained partition_dir/index_dir/ layer_dir as the single source of truth for a partition's on-disk layout, replacing per-module duplicated const INDEX_SUBDIR: &str = "index" (7 copies) and ad hoc path joins — including one found duplicated inside KmerPartition itself (ensure_writer rebuilt part_dir's own logic by hand).
• KmerPartition gained partition_meta/n_layers/index_mode, wrapping obilayeredmap::meta::PartitionMeta::load (via the existing common::load_meta, which also recovers indexes built before meta.json existed). Before this, obikphylo and obikindex imported obilayeredmap::meta::PartitionMeta directly and called ::load() themselves at 21 call sites, each redoing its own error-mapping — every one of those crates knew the on-disk metadata format instead of going through an interface. Fixed everywhere except one remaining spot (below). Caught as a side effect: dump_layer.rs/query_layer.rs had been calling PartitionMeta::load directly, bypassing load_meta entirely — they never got the missing-meta.json recovery the other callers did.
• Layer introspection API discussed but not yet implemented — three axes, deliberately kept separate after an initial draft conflated them:
  • LayerContent { Count, Presence } — what the layer stores; a const on LayerData (compile-time, zero-cost), not a runtime field.
  • StorageKind { Implicit, Columnar, Packed, Sparse } — how it's stored; only meaningful for D that actually carry data (Layer<()> has neither this nor LayerContent — it's a write-time-only state, never a queryable content: once a layer is closed, "no matrix file" reads back as Presence/Implicit via PersistentBitMatrix::open's own fallback, not as some third "empty" content).
  • EvidenceKind { Exact, Approx, Hybrid } — from MphfLayer's own already-in-memory LayerEvidence discriminant.
  • Not all (LayerContent, StorageKind) pairs are legal: Count never has Implicit or Sparse.

Implemented (2026-08-20). LayerContent/StorageKind/EvidenceKind now exist, each with two forms:

• A runtime accessor on an already-open value (Layer<D>::content()/ storage_kind()/evidence_kind(), PersistentBitMatrix::storage_kind(), PersistentCompactIntMatrix::storage_kind(), MphfLayer::evidence_kind()) — reads a discriminant already in memory, zero disk access.
• A lightweight detect()/detect_storage() disk probe that mirrors the corresponding open()'s own priority order by hand (file-existence checks only, no mmap) — usable before committing to a D, unlike the runtime accessors. Exposed per-layer on LayeredMap<D> as detect_layer_content/detect_layer_storage/detect_layer_evidence (work regardless of D, since they only use self.root + the layer index).

StorageKind lives in obicompactvec (owner of PersistentBitMatrix/ PersistentCompactIntMatrix); LayerContent/EvidenceKind live in obilayeredmap. HasLayerContent/HasStorageKind gate Layer<()> out of content()/storage_kind() (no matrix, nothing to report), matching the "empty is transitional" conclusion above. 42 new tests across obilayeredmap's tests/layer.rs and tests/map.rs; full workspace suite green (0 failed) after.

Not done: these detect() probes don't yet replace Mat::open's or QueryLayer::open's own hand-rolled equivalents (still duplicated content/ storage decisions, now a third copy of the same logic to keep in sync) — that consolidation is (1)/(2)'s job, not this prep step's.

One bug found while reading around this (signalled, not fixed); one earlier claim retracted

• obicompactvec::bitmatrix::sparse.rs's module doc says "Not used by any production code path yet" — false since obikmer pack --sparse (cmd/pack/mod.rs) is wired to pack_sparse_bit_matrix and Mat::open already reads the result back in the sibling-annex path. Stale comment, not corrected.
• Retracted (2026-08-20): an earlier pass through this doc claimed obikpartition::query_layer::QueryLayer::open had no sparse-format detection and would silently corrupt reads on a pack --sparsed layer. False — PersistentBitMatrix (obicompactvec::bitmatrix::persistent) is a 4-way enum (Columnar/Packed/Sparse/Implicit), not 3-way as first read; its open() already detects Sparse via presence/sparse_meta.json, and every method on the type (row, fill_row, nonzero_iter, …) already dispatches all 4 arms. QueryLayer::open's PersistentBitMatrix::open(layer_dir) call was never the bug. Root cause of the false claim: a grep -n "Implicit\|Columnar\|Packed" used to read the enum definition silently skipped the Sparse(...) line because it matched none of those three words — a self-inflicted blind spot from a filtered read, not a fact about the code. Lesson: for a pub enum whose variant list matters, read the definition unfiltered, don't grep for the variant names you expect to find.
• One real consequence of that same correction, fixed (2026-08-20): obikphylo::siblings::cache::Mat::SparsePresence(Layer< PersistentSparseBitMatrix>) was redundant — Mat::Presence(Layer< PersistentBitMatrix>) alone already handles sparse layers transparently, since PersistentBitMatrix absorbs Sparse internally. Removed the variant, the presence/is_multi.prsb probe in Mat::open (now just opens Layer::<PersistentBitMatrix> unconditionally for the non-count case — sparse-vs-dense is PersistentBitMatrix::open's own concern), and every now-single-armed match in find_slot/index_batch/ iter_minorants_batch/n_cols/fill_sub_matrix_carries. Full workspace test suite green after, including the 27 obikphylo::siblings tests that exercise pack_matrices(true)/sparse through Mat.

Remaining instance of the PartitionMeta-encapsulation problem

obikphylo::siblings::family_scan::scan_layer_families still re-derives index_dir from layer_dir.parent() and calls PartitionMeta::load itself, purely to get .mode for Mat::open. Fixing it the way the 21 other call sites were fixed needs more than a 1:1 swap: scan_layer_families only receives a bare layer_dir: &Path, not a (partition, part, layer) triple, and its single upstream source of layer paths, sibling_layer_dirs, returns a flat Vec<PathBuf> with the partition/layer indices already discarded. Fixing it properly means either having sibling_layer_dirs return (PathBuf, IndexMode) (or (part, layer)) pairs, or threading &KmerPartition + indices through instead of paths — and touching every one of scan_layer_families's 8 callers (distance.rs, alignment.rs, cardinality.rs, entropy.rs ×2, sankoff_bundle.rs ×2, stats.rs). Left alone this round; worth doing as part of the same pass that builds (1)/(2), since those callers are exactly the sibling-annex consumers (2) is meant to serve.