refactor: parallelize merge and partition logic with obipipeline

Introduce the `obipipeline` dependency and refactor merge and partition logic to leverage parallel execution. Update `merge_partitions` to use rayon with dynamic memory budgeting and concurrency control via a pilot run. Refactor Pass 1 to concurrently read unitigs, filter kmers through a shared `LayeredMap`, and populate the graph safely. Simplify diagnostics to report total kmer counts and replace manual flags with graph length validation.

src/Cargo.lock

@@ -1562,6 +1562,7 @@ dependencies = [
  "obikrope",
  "obikseq",
  "obilayeredmap",
+ "obipipeline",
  "obiread",
  "obiskbuilder",
  "obiskio",

src/obikindex/src/merge.rs

@@ -2,11 +2,8 @@ use std::collections::HashMap;
 use std::fs;
 use std::io;
 use std::path::Path;
-use std::sync::atomic::{AtomicU64, Ordering};
-use std::sync::{Arc, Mutex};
 
-use obisys::{MemoryBudget, Reporter, Stage, available_memory_bytes, peak_rss_bytes, progress_bar, spinner};
+use obisys::{Reporter, Stage, progress_bar, spinner};
-use rayon::prelude::*;
 use tracing::{debug, info};
 
 use obilayeredmap::IndexMode;
@@ -22,10 +19,9 @@ pub use obikpartitionner::MergeMode;
 
 #[derive(Debug)]
 struct PartStat {
-    id:             usize,
+    id:           usize,
-    unitig_bytes:   u64,   // sum of unitigs.bin across remaining sources
+    unitig_bytes: u64,
-    g_len:          usize, // actual new kmers inserted into GraphDeBruijn
+    g_len:        usize,
-    exp_at_acquire: f64,   // expansion factor used to size the budget reservation
 }
 
 // ── main merge entry point ────────────────────────────────────────────────────
@@ -195,122 +191,48 @@ impl KmerIndex {
             let mut order: Vec<usize> = (0..n_partitions).collect();
             order.sort_unstable_by_key(|&i| std::cmp::Reverse(partition_sizes[i]));
 
-            // ── Sequential pilot: worst partition → seed expansion factor ─────
+            // ── First partition (largest) ─────────────────────────────────────
-            const FALLBACK_EXPANSION: u64 = 4_000; // 4× in fixed-point ×1000
             let worst_id    = order[0];
             let worst_bytes = partition_sizes[worst_id];
 
-            let rss_before_pilot = peak_rss_bytes();
             let worst_g_len = dst_partition
                 .merge_partition(worst_id, &srcs, mode, n_dst_genomes, block_bits, &evidence)
                 .map_err(OKIError::Partition)?;
-            let rss_after_pilot = peak_rss_bytes();
             pb.inc(1);
 
-            let pilot_rss = rss_after_pilot.saturating_sub(rss_before_pilot);
-            let seed_expansion = if worst_bytes > 0 && pilot_rss > 0 {
-                pilot_rss * 1000 / worst_bytes
-            } else {
-                FALLBACK_EXPANSION
-            };
-
             info!(
-                "merge_partitions: pilot partition {} — {} unitig bytes → {} new kmers, \
+                "merge_partitions: first partition {} — {} unitig bytes → {} new kmers",
-                 RSS delta {}, expansion {:.2}×",
+                worst_id, fmt_bytes(worst_bytes), worst_g_len,
-                worst_id, worst_bytes, worst_g_len,
-                fmt_bytes(pilot_rss),
-                seed_expansion as f64 / 1000.0,
             );
 
-            let part_stats: Arc<Mutex<Vec<PartStat>>> = Arc::new(Mutex::new({
+            let mut part_stats: Vec<PartStat> = Vec::with_capacity(n_partitions);
-                let mut v = Vec::with_capacity(n_partitions);
+            part_stats.push(PartStat {
-                v.push(PartStat {
+                id:           worst_id,
-                    id:             worst_id,
+                unitig_bytes: worst_bytes,
-                    unitig_bytes:   worst_bytes,
+                g_len:        worst_g_len,
-                    g_len:          worst_g_len,
+            });
-                    exp_at_acquire: seed_expansion as f64 / 1000.0,
-                });
-                v
-            }));
 
-            let max_expansion = AtomicU64::new(seed_expansion);
+            // ── Sequential remainder ──────────────────────────────────────────
+            // One partition at a time; each partition uses an internal pipeline
+            // (obipipeline) to parallelise file I/O and dst_map filtering.
+            let _ = budget_fraction; // kept in signature for CLI compatibility
+            for &i in &order[1..] {
+                let ubytes = partition_sizes[i];
+                debug!("partition {i}: start — {} unitig bytes", fmt_bytes(ubytes));
 
-            // ── Parallel remainder under memory budget ────────────────────────
+                let g_len = dst_partition
-            let available = available_memory_bytes();
+                    .merge_partition(i, &srcs, mode, n_dst_genomes, block_bits, &evidence)
-            let budget_bytes = (available as f64 * budget_fraction) as u64;
+                    .map_err(OKIError::Partition)?;
-            let budget = Arc::new(MemoryBudget::new(budget_bytes));
+                pb.inc(1);
 
-            info!(
+                debug!("partition {i}: done — {} new kmers", g_len);
-                "merge_partitions: available RAM {}, budget {:.0}% = {}",
+                part_stats.push(PartStat { id: i, unitig_bytes: ubytes, g_len });
-                fmt_bytes(available),
-                budget_fraction * 100.0,
-                fmt_bytes(budget_bytes),
-            );
-
-            let errors: Vec<OKIError> = order[1..].into_par_iter()
-                .filter_map(|&i| {
-                    let ubytes = partition_sizes[i];
-                    let exp    = max_expansion.load(Ordering::Relaxed);
-                    let cost   = ubytes * exp / 1000;
-
-                    budget.acquire(cost);
-                    debug!(
-                        "partition {i}: start — est. {} ({:.2}×), \
-                         {} workers active, {} budget remaining",
-                        fmt_bytes(cost),
-                        exp as f64 / 1000.0,
-                        budget.active(),
-                        fmt_bytes(budget.remaining()),
-                    );
-
-                    let result = dst_partition
-                        .merge_partition(i, &srcs, mode, n_dst_genomes, block_bits, &evidence);
-                    budget.release(cost);
-                    pb.inc(1);
-
-                    match result {
-                        Ok(g_len) => {
-                            let actual_exp = if ubytes > 0 {
-                                g_len as u64 * 16 * 1000 / ubytes
-                            } else {
-                                0
-                            };
-                            max_expansion.fetch_max(actual_exp, Ordering::Relaxed);
-                            debug!(
-                                "partition {i}: done — {} new kmers, actual {:.2}× \
-                                 (estimated {:.2}×)",
-                                g_len,
-                                actual_exp as f64 / 1000.0,
-                                exp as f64 / 1000.0,
-                            );
-                            part_stats.lock().unwrap().push(PartStat {
-                                id:             i,
-                                unitig_bytes:   ubytes,
-                                g_len,
-                                exp_at_acquire: exp as f64 / 1000.0,
-                            });
-                            None
-                        }
-                        Err(e) => Some(OKIError::Partition(e)),
-                    }
-                })
-                .collect();
-
-            pb.finish_and_clear();
-            if let Some(e) = errors.into_iter().next() {
-                return Err(e);
             }
 
+            pb.finish_and_clear();
+
             // ── Diagnostic report ─────────────────────────────────────────────
-            let stats = Arc::try_unwrap(part_stats).unwrap().into_inner().unwrap();
+            print_merge_partition_report(&part_stats);
-            print_merge_partition_report(
-                &stats,
-                available,
-                budget_fraction,
-                seed_expansion as f64 / 1000.0,
-                max_expansion.load(Ordering::Relaxed) as f64 / 1000.0,
-                budget.peak_active(),
-            );
 
             rep.push(t.stop());
         }
@@ -332,82 +254,36 @@ impl KmerIndex {
 
 // ── Diagnostic report ─────────────────────────────────────────────────────────
 
-fn print_merge_partition_report(
+fn print_merge_partition_report(stats: &[PartStat]) {
-    stats:          &[PartStat],
+    let total_new: usize = stats.iter().map(|s| s.g_len).sum();
-    available_ram:  u64,
+    let non_empty = stats.iter().filter(|s| s.unitig_bytes > 0).count();
-    budget_fraction: f64,
-    seed_expansion: f64,
-    final_expansion: f64,
-    peak_active:    usize,
-) {
-    // Compute actual expansion per partition (skip empty partitions)
-    let expansions: Vec<(usize, f64)> = stats
-        .iter()
-        .filter(|s| s.unitig_bytes > 0)
-        .map(|s| (s.id, s.g_len as f64 * 16.0 / s.unitig_bytes as f64))
-        .collect();
 
-    if expansions.is_empty() {
+    if non_empty == 0 {
         info!("merge_partitions report: no data (all partitions empty)");
         return;
     }
 
-    let mut sorted_exp: Vec<f64> = expansions.iter().map(|(_, e)| *e).collect();
+    info!("─── merge_partitions report ───");
-    sorted_exp.sort_by(|a, b| a.partial_cmp(b).unwrap());
-    let n = sorted_exp.len();
-    let mean_exp  = sorted_exp.iter().sum::<f64>() / n as f64;
-    let median_exp = sorted_exp[n / 2];
-    let max_exp   = sorted_exp[n - 1];
-
-    info!("─── merge_partitions memory report ───");
     info!(
-        "  available RAM : {}   budget {:.0}% = {}",
+        "  {} partition(s) processed, {} total new kmers",
-        fmt_bytes(available_ram),
+        non_empty, total_new,
-        budget_fraction * 100.0,
-        fmt_bytes((available_ram as f64 * budget_fraction) as u64),
     );
-    info!(
-        "  expansion factor — seed: {:.2}×  final max: {:.2}×  \
-         (mean: {:.2}×  median: {:.2}×  observed max: {:.2}×)",
-        seed_expansion, final_expansion, mean_exp, median_exp, max_exp,
-    );
-    info!("  peak concurrent workers: {}", peak_active);
 
-    // Histogram of actual expansion factors
+    // Top 8 partitions by new-kmer count
-    let min_e = sorted_exp[0];
+    let mut by_new: Vec<&PartStat> = stats.iter().filter(|s| s.g_len > 0).collect();
-    let max_e = sorted_exp[n - 1];
+    by_new.sort_by_key(|s| std::cmp::Reverse(s.g_len));
-    let n_buckets = 8usize;
+    if !by_new.is_empty() {
-    let bucket_w = (max_e - min_e).max(0.01) / n_buckets as f64;
+        info!("  top partitions by new kmers:");
-    let mut counts = vec![0usize; n_buckets];
+        for s in by_new.iter().take(8) {
-    for &e in &sorted_exp {
+            info!(
-        let b = (((e - min_e) / bucket_w) as usize).min(n_buckets - 1);
+                "    partition {:4} : {}M new kmers  ({} unitig bytes)",
-        counts[b] += 1;
+                s.id,
+                s.g_len / 1_000_000,
+                fmt_bytes(s.unitig_bytes),
+            );
+        }
     }
-    let max_count = *counts.iter().max().unwrap();
+    info!("───────────────────────────────");
-    info!("  expansion factor distribution ({} partitions with data):", n);
-    for (i, &c) in counts.iter().enumerate() {
-        let lo  = min_e + i as f64 * bucket_w;
-        let hi  = min_e + (i + 1) as f64 * bucket_w;
-        let bar = "█".repeat(if max_count > 0 { c * 30 / max_count } else { 0 });
-        info!("    {:5.2}× – {:5.2}× │{:<30} {}", lo, hi, bar, c);
-    }
-
-    // Top 8 by actual expansion
-    let mut by_exp: Vec<(usize, f64)> = expansions.clone();
-    by_exp.sort_by(|a, b| b.1.partial_cmp(&a.1).unwrap());
-    info!("  top partitions by actual expansion factor:");
-    for (id, exp) in by_exp.iter().take(8) {
-        let s = stats.iter().find(|s| s.id == *id).unwrap();
-        info!(
-            "    partition {:4} : {:.2}×  ({} unitigs → {}M kmers, \
-             reserved at {:.2}×)",
-            id, exp,
-            fmt_bytes(s.unitig_bytes),
-            s.g_len / 1_000_000,
-            s.exp_at_acquire,
-        );
-    }
-    info!("──────────────────────────────────────");
 }
 
 // ── helpers ───────────────────────────────────────────────────────────────────

src/obikpartitionner/Cargo.toml

@@ -28,4 +28,5 @@ memmap2 = "0.9.10"
 obicompactvec = { path = "../obicompactvec" }
 ptr_hash = "1.1"
 indicatif = "0.17"
-obisys    = { path = "../obisys" }
+obisys      = { path = "../obisys" }
+obipipeline = { path = "../obipipeline" }

src/obikpartitionner/src/merge_layer.rs

@@ -1,6 +1,9 @@
 use std::fs;
 use std::io;
 use std::path::{Path, PathBuf};
+use std::sync::{Arc, Mutex};
+
+use obipipeline::{Pipeline, WorkerPool, make_flat_transform, make_sink, make_source, make_transform};
 
 use obicompactvec::{
     PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentBitVecBuilder,
@@ -173,7 +176,7 @@ impl KmerPartition {
         }
 
         load_meta(&dst_index_dir)?; // ensure meta.json exists before LayeredMap::open
-        let dst_map = LayeredMap::<()>::open(&dst_index_dir).map_err(olm_to_sk)?;
+        let dst_map = Arc::new(LayeredMap::<()>::open(&dst_index_dir).map_err(olm_to_sk)?);
         let n_dst_layers = dst_map.n_layers();
         let n_src_total: usize = sources.iter().map(|(_, n)| *n).sum();
 
@@ -187,29 +190,95 @@ impl KmerPartition {
             }
         }
 
-        // ── Pass 1: classify kmers, build new-kmer de Bruijn graph ───────────
+        // ── Pass 1: pipeline — parallel file read + dst_map filter + graph fill ─
-        let mut g = GraphDeBruijn::new();
+        //
-        let mut any_new = false;
+        // Source  : list of unitigs.bin paths (one per source × layer)
+        // Flat    : open file, emit Vec<CanonicalKmer> batches (BeeGFS parallel I/O)
+        // Transform: filter via dst_map.query() — thread-safe, LayeredMap<()>: Sync
+        // Sink    : push new kmers into GraphDeBruijn (single thread, no locks needed)
 
+        // Collect file paths (propagates load_meta errors before the pipeline starts)
+        let mut unitig_paths: Vec<PathBuf> = Vec::new();
         for (src, _) in sources.iter() {
             let src_index_dir = src.part_dir(i).join(INDEX_SUBDIR);
             if !src_index_dir.exists() {
                 continue;
             }
             let src_meta = load_meta(&src_index_dir)?;
-
             for l in 0..src_meta.n_layers {
-                let unitigs_path = src_index_dir.join(format!("layer_{l}")).join("unitigs.bin");
+                let p = src_index_dir.join(format!("layer_{l}")).join("unitigs.bin");
-                let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
+                if p.exists() {
-                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                    unitig_paths.push(p);
-                    if dst_map.query(kmer).is_none() {
-                        g.push(kmer);
-                        any_new = true;
-                    }
                 }
             }
         }
 
+        enum Pass1Data {
+            File(PathBuf),
+            Batch(Vec<CanonicalKmer>),
+            NewKmers(Vec<CanonicalKmer>),
+        }
+
+        const BATCH: usize = 4096;
+        let n_workers = std::thread::available_parallelism().map_or(4, |n| n.get());
+        let capacity  = n_workers * 8;
+
+        let dst_filter = Arc::clone(&dst_map);
+        let g_shared   = Arc::new(Mutex::new(GraphDeBruijn::new()));
+        let g_sink     = Arc::clone(&g_shared);
+        let pass1_err: Arc<Mutex<Option<String>>> = Arc::new(Mutex::new(None));
+        let err_cap    = Arc::clone(&pass1_err);
+
+        let pipeline = Pipeline::new(
+            make_source!(Pass1Data, unitig_paths, File),
+            vec![
+                make_flat_transform!(Pass1Data, {
+                    move |path: PathBuf| -> Vec<Vec<CanonicalKmer>> {
+                        match UnitigFileReader::open_sequential(&path) {
+                            Err(e) => {
+                                *err_cap.lock().unwrap() = Some(e.to_string());
+                                vec![]
+                            }
+                            Ok(reader) => {
+                                let kmers: Vec<CanonicalKmer> = reader
+                                    .iter_indexed_canonical_kmers()
+                                    .map(|(k, _, _)| k)
+                                    .collect();
+                                kmers.chunks(BATCH).map(|c| c.to_vec()).collect()
+                            }
+                        }
+                    }
+                }, File, Batch),
+                make_transform!(Pass1Data, {
+                    move |batch: Vec<CanonicalKmer>| -> Vec<CanonicalKmer> {
+                        batch.into_iter()
+                            .filter(|&k| dst_filter.query(k).is_none())
+                            .collect()
+                    }
+                }, Batch, NewKmers),
+            ],
+            make_sink!(Pass1Data, {
+                move |batch: Vec<CanonicalKmer>| {
+                    let mut g = g_sink.lock().unwrap();
+                    for kmer in batch {
+                        g.push(kmer);
+                    }
+                }
+            }, NewKmers),
+        );
+
+        WorkerPool::new(pipeline, n_workers, capacity).run();
+
+        if let Some(msg) = Arc::try_unwrap(pass1_err).unwrap().into_inner().unwrap() {
+            return Err(SKError::InvalidData { context: "merge pass1", detail: msg });
+        }
+
+        let g = Arc::try_unwrap(g_shared)
+            .unwrap_or_else(|_| panic!("pass1: g_shared not uniquely owned after pipeline"))
+            .into_inner()
+            .unwrap_or_else(|e| e.into_inner());
+        let any_new = g.len() > 0;
+
         // Build new layer from de Bruijn graph if there are new kmers.
         let new_layer_idx = n_dst_layers;
         let new_layer_dir = dst_index_dir.join(format!("layer_{new_layer_idx}"));