diff --git a/src/obidebruinj/src/debruijn.rs b/src/obidebruinj/src/debruijn.rs index a435d83..23c1a1c 100644 --- a/src/obidebruinj/src/debruijn.rs +++ b/src/obidebruinj/src/debruijn.rs @@ -1,15 +1,15 @@ //use ahash::RandomState; +use crossbeam_channel; use hashbrown::HashMap; use obikseq::k; use obikseq::{CanonicalKmer, Sequence, Unitig}; use rayon::iter::{IntoParallelRefIterator, ParallelIterator}; use std::cell::RefCell; use std::fmt; -use crossbeam_channel; use std::sync::atomic::{AtomicU8, Ordering}; -use xxhash_rust::xxh3::Xxh3Builder; use std::time::Instant; use tracing::{debug, info}; +use xxhash_rust::xxh3::Xxh3Builder; // ── Types ───────────────────────────────────────────────────────────────────── @@ -99,7 +99,6 @@ impl Node { (self.0 >> 5) & 0b11 } - /// Marks the node as visited. #[inline] pub fn set_visited(&mut self) { @@ -180,8 +179,12 @@ impl WalkState { } pub fn reachable(&self, graph: &GraphDeBruijn) -> bool { - WalkState { kmer: self.kmer, node: self.node, direct: !self.direct } - .leavable(graph) + WalkState { + kmer: self.kmer, + node: self.node, + direct: !self.direct, + } + .leavable(graph) } pub fn walk(&self, graph: &GraphDeBruijn) -> Option<(WalkState, u8)> { @@ -197,8 +200,19 @@ impl WalkState { if next_node.is_visited() { return None; } - let reachable = if dnext { next_node.can_extend_left() } else { next_node.can_extend_right() }; - reachable.then_some((WalkState { kmer: cnext, node: next_node, direct: dnext }, nuc)) + let reachable = if dnext { + next_node.can_extend_left() + } else { + next_node.can_extend_right() + }; + reachable.then_some(( + WalkState { + kmer: cnext, + node: next_node, + direct: dnext, + }, + nuc, + )) } else { if !self.node.can_extend_left() { return None; @@ -211,8 +225,19 @@ impl WalkState { if next_node.is_visited() { return None; } - let reachable = if dnext { next_node.can_extend_right() } else { next_node.can_extend_left() }; - reachable.then_some((WalkState { kmer: cnext, node: next_node, direct: dnext }, 3 - nuc)) + let reachable = if dnext { + next_node.can_extend_right() + } else { + next_node.can_extend_left() + }; + reachable.then_some(( + WalkState { + kmer: cnext, + node: next_node, + direct: dnext, + }, + 3 - nuc, + )) } } } @@ -275,7 +300,11 @@ impl GraphDeBruijn { node.set_left(lc, ln); atomic.store(node.0, Ordering::Relaxed); }); - debug!("[compute_degrees] pass 1 (degrees): {:?} — {} nodes", t1.elapsed(), self.nodes.len()); + debug!( + "[compute_degrees] pass 1 (degrees): {:?} — {} nodes", + t1.elapsed(), + self.nodes.len() + ); // Pass 2: mark start nodes @@ -290,7 +319,11 @@ impl GraphDeBruijn { atomic.store(node.0, Ordering::Relaxed); } }); - debug!("[compute_degrees] pass 2 (starts): {:?} — {} nodes", t2.elapsed(), self.nodes.len()); + debug!( + "[compute_degrees] pass 2 (starts): {:?} — {} nodes", + t2.elapsed(), + self.nodes.len() + ); } pub fn is_visited(&self, kmer: &CanonicalKmer) -> Option { @@ -328,14 +361,28 @@ impl GraphDeBruijn { } fn unitig_nucleotides(&self, kmer: CanonicalKmer, k: usize) -> Option> { - let old = self.nodes.get(&kmer)?.fetch_or(IS_VISITED_MASK, Ordering::AcqRel); - if old & IS_VISITED_MASK != 0 { return None; } + let old = self + .nodes + .get(&kmer)? + .fetch_or(IS_VISITED_MASK, Ordering::AcqRel); + if old & IS_VISITED_MASK != 0 { + return None; + } let start = WalkState::new(kmer, Node(old), true); let next_step = start.walk(self).and_then(|(next_state, nuc)| { - let ext_old = self.nodes.get(&next_state.kmer)?.fetch_or(IS_VISITED_MASK, Ordering::AcqRel); + let ext_old = self + .nodes + .get(&next_state.kmer)? + .fetch_or(IS_VISITED_MASK, Ordering::AcqRel); (ext_old & IS_VISITED_MASK == 0).then_some((next_state, nuc)) }); - Some(UnitigNucIter { graph: self, start: kmer, pos: 0, k, next_step }) + Some(UnitigNucIter { + graph: self, + start: kmer, + pos: 0, + k, + next_step, + }) } pub fn for_each_unitig(&self, f: impl Fn(UnitigNucIter<'_>) + Sync) { @@ -352,7 +399,9 @@ impl GraphDeBruijn { self.nodes .par_iter() .filter_map(|(&kmer, atomic)| { - Node(atomic.load(Ordering::Acquire)).is_start().then_some(kmer) + Node(atomic.load(Ordering::Acquire)) + .is_start() + .then_some(kmer) }) .for_each(|kmer| { if let Some(iter) = self.unitig_nucleotides(kmer, k) { @@ -403,10 +452,10 @@ impl GraphDeBruijn { } } - info!( + debug!( chains = n_chains.load(Ordering::Relaxed), phase2 = n2.load(Ordering::Relaxed), - total = n_chains.load(Ordering::Relaxed) + n2.load(Ordering::Relaxed), + total = n_chains.load(Ordering::Relaxed) + n2.load(Ordering::Relaxed), "unitig traversal complete" ); } @@ -508,7 +557,11 @@ impl Iterator for UnitigNucIter<'_> { Some(nuc) } else if let Some((state, nuc)) = self.next_step.take() { self.next_step = state.walk(self.graph).and_then(|(next_state, next_nuc)| { - let old = self.graph.nodes.get(&next_state.kmer)?.fetch_or(IS_VISITED_MASK, Ordering::AcqRel); + let old = self + .graph + .nodes + .get(&next_state.kmer)? + .fetch_or(IS_VISITED_MASK, Ordering::AcqRel); (old & IS_VISITED_MASK == 0).then_some((next_state, next_nuc)) }); Some(nuc) @@ -539,10 +592,16 @@ fn count_neighbors( } nuc = i as u8; count += 1; - if count >= 2 { return (2, None); } + if count >= 2 { + return (2, None); + } } } - if count == 1 { (1, Some(nuc)) } else { (0, None) } + if count == 1 { + (1, Some(nuc)) + } else { + (0, None) + } } // ── tests ───────────────────────────────────────────────────────────────────── diff --git a/src/obikindex/src/merge.rs b/src/obikindex/src/merge.rs index fa990d8..f32fc8f 100644 --- a/src/obikindex/src/merge.rs +++ b/src/obikindex/src/merge.rs @@ -21,9 +21,9 @@ pub use obikpartitionner::MergeMode; #[derive(Debug)] struct PartStat { - id: usize, + id: usize, unitig_bytes: u64, - g_len: usize, + g_len: usize, } // ── main merge entry point ──────────────────────────────────────────────────── @@ -53,9 +53,9 @@ impl KmerIndex { if src.state() != IndexState::Indexed { return Err(OKIError::NotIndexed(src.root_path.clone())); } - if src.kmer_size() != ref0.kmer_size() - || src.minimizer_size() != ref0.minimizer_size() - || src.n_partitions() != ref0.n_partitions() + if src.kmer_size() != ref0.kmer_size() + || src.minimizer_size() != ref0.minimizer_size() + || src.n_partitions() != ref0.n_partitions() { return Err(OKIError::IncompatibleConfig); } @@ -65,39 +65,65 @@ impl KmerIndex { } // ── Log source characteristics and choose base ──────────────────────── - let mode_str = if mode == MergeMode::Presence { "presence" } else { "count" }; + let mode_str = if mode == MergeMode::Presence { + "presence" + } else { + "count" + }; info!( "merge: {} source(s), smer-size={}, mode={}", - sources.len(), sources[0].kmer_size(), mode_str, + sources.len(), + sources[0].kmer_size(), + mode_str, ); for (i, src) in sources.iter().enumerate() { - let genome_str = if src.meta.genomes.len() == 1 { "mono-genome".to_string() } - else { format!("{} genomes", src.meta.genomes.len()) }; - let trivial_str = if is_trivial(src, mode) { " [trivial: no data approximation]" } else { "" }; + let genome_str = if src.meta.genomes.len() == 1 { + "mono-genome".to_string() + } else { + format!("{} genomes", src.meta.genomes.len()) + }; + let trivial_str = if is_trivial(src, mode) { + " [trivial: no data approximation]" + } else { + "" + }; info!( " [{}] {} — {}, {}, {}{}", - i, src.root_path.display(), + i, + src.root_path.display(), format_evidence(&src.meta.config.evidence), - genome_str, mode_str, trivial_str, + genome_str, + mode_str, + trivial_str, ); } let base_idx = choose_base(sources, mode); let needs_approx = sources.iter().any(|src| { !is_trivial(src, mode) - && matches!(src.meta.config.evidence, IndexMode::Approx { .. } | IndexMode::Hybrid { .. }) + && matches!( + src.meta.config.evidence, + IndexMode::Approx { .. } | IndexMode::Hybrid { .. } + ) }); info!( "output evidence: {} ({}base: [{}] {})", format_evidence(&sources[base_idx].meta.config.evidence), - if needs_approx { "forced approx — " } else { "" }, - base_idx, sources[base_idx].root_path.display(), + if needs_approx { + "forced approx — " + } else { + "" + }, + base_idx, + sources[base_idx].root_path.display(), ); let mut ordered: Vec<&KmerIndex> = Vec::with_capacity(sources.len()); ordered.push(sources[base_idx]); for (i, &src) in sources.iter().enumerate() { - if i != base_idx { ordered.push(src); } + if i != base_idx { + ordered.push(src); + } } let sources: &[&KmerIndex] = &ordered; let evidence = sources[0].meta.config.evidence.clone(); @@ -151,7 +177,8 @@ impl KmerIndex { fs::remove_dir_all(&spectrums_dir)?; } for (src, new_labels) in sources.iter().zip(&source_labels) { - let old_labels: Vec = src.meta.genomes.iter().map(|g| g.label.clone()).collect(); + let old_labels: Vec = + src.meta.genomes.iter().map(|g| g.label.clone()).collect(); copy_spectrums(&src.root_path, output, &old_labels, new_labels)?; } pb.finish_and_clear(); @@ -184,9 +211,12 @@ impl KmerIndex { // Per-partition unitig byte sizes across remaining sources (stat() only) let partition_sizes: Vec = (0..n_partitions) - .map(|i| remaining_sources.iter() - .map(|s| partition_unitig_bytes(s, i)) - .sum()) + .map(|i| { + remaining_sources + .iter() + .map(|s| partition_unitig_bytes(s, i)) + .sum() + }) .collect(); // LFD sort: largest partition first @@ -201,7 +231,8 @@ impl KmerIndex { // IDs; each reports (id, g_len, duration) on a result channel. const SPAWN_THRESHOLD: f64 = 0.95; // spawn when >5% capacity idle let n_cores = std::thread::available_parallelism() - .map(|n| n.get()).unwrap_or(1); + .map(|n| n.get()) + .unwrap_or(1); let max_workers = (n_cores / 2).max(1); let _ = budget_fraction; // kept in signature for CLI compatibility @@ -220,6 +251,9 @@ impl KmerIndex { let mut part_stats: Vec = Vec::with_capacity(n_partitions); let mut n_workers = 0usize; let mut cpu_sample = CpuSample::now(); + // Efficiency measured just before each spawn, used to assess + // whether the previous worker delivered its expected marginal gain. + let mut efficiency_at_last_spawn = 0.0f64; // Shadow as references so closures can capture them by copy. let srcs = &srcs; @@ -237,7 +271,12 @@ impl KmerIndex { for i in &prx { let t = Instant::now(); let r = dst_partition.merge_partition( - i, srcs, mode, n_dst_genomes, block_bits, evidence, + i, + srcs, + mode, + n_dst_genomes, + block_bits, + evidence, ); rtx.send((i, r, t.elapsed())).ok(); } @@ -252,26 +291,51 @@ impl KmerIndex { let mut completed = 0usize; while completed < n_partitions { - let (i, r, dur) = result_rx.recv() - .map_err(|_| OKIError::Io(io::Error::new( - io::ErrorKind::UnexpectedEof, "worker channel closed")))?; + let (i, r, dur) = result_rx.recv().map_err(|_| { + OKIError::Io(io::Error::new( + io::ErrorKind::UnexpectedEof, + "worker channel closed", + )) + })?; let g_len = r.map_err(OKIError::Partition)?; pb.inc(1); - debug!("partition {i}: done in {:.1}s — {} new kmers", - dur.as_secs_f64(), g_len); + debug!( + "partition {i}: done in {:.1}s — {} new kmers", + dur.as_secs_f64(), + g_len + ); part_stats.push(PartStat { - id: i, unitig_bytes: partition_sizes[i], g_len, + id: i, + unitig_bytes: partition_sizes[i], + g_len, }); completed += 1; if n_workers < max_workers && completed < n_partitions { let eff = cpu_sample.cpu_efficiency(n_cores); - if eff < SPAWN_THRESHOLD { + // For the first spawn use SPAWN_THRESHOLD. + // For subsequent spawns: the previous worker should + // have raised efficiency by at least a quarter of the expected + // marginal gain (1/n_workers). If not, adding another + // worker won't help. + let should_spawn = if n_workers == 1 { + eff < SPAWN_THRESHOLD + } else { + let gain = eff - efficiency_at_last_spawn; + let expected = 1.0 / n_workers as f64; + gain >= expected * 0.25 + }; + if should_spawn { + debug!( + "activated worker {} — efficiency {:.0}%, gain vs prev {:.0}%", + n_workers + 1, + eff * 100.0, + (eff - efficiency_at_last_spawn) * 100.0, + ); + efficiency_at_last_spawn = eff; activate_tx.send(()).ok(); n_workers += 1; cpu_sample = CpuSample::now(); - debug!("activated worker {n_workers} — efficiency {:.0}%", - eff * 100.0); } } } @@ -319,9 +383,7 @@ fn print_merge_partition_report(stats: &[PartStat], n_workers: usize, max_worker " {} partition(s) processed, {} total new kmers", non_empty, total_new, ); - info!( - " workers spawned: {n_workers} / {max_workers} (max)", - ); + info!(" workers spawned: {n_workers} / {max_workers} (max)",); // Top 8 partitions by new-kmer count let mut by_new: Vec<&PartStat> = stats.iter().filter(|s| s.g_len > 0).collect(); @@ -343,10 +405,15 @@ fn print_merge_partition_report(stats: &[PartStat], n_workers: usize, max_worker // ── helpers ─────────────────────────────────────────────────────────────────── fn fmt_bytes(b: u64) -> String { - if b >= 1 << 30 { format!("{:.1} GB", b as f64 / (1u64 << 30) as f64) } - else if b >= 1 << 20 { format!("{:.1} MB", b as f64 / (1u64 << 20) as f64) } - else if b >= 1 << 10 { format!("{:.1} KB", b as f64 / (1u64 << 10) as f64) } - else { format!("{b} B") } + if b >= 1 << 30 { + format!("{:.1} GB", b as f64 / (1u64 << 30) as f64) + } else if b >= 1 << 20 { + format!("{:.1} MB", b as f64 / (1u64 << 20) as f64) + } else if b >= 1 << 10 { + format!("{:.1} KB", b as f64 / (1u64 << 10) as f64) + } else { + format!("{b} B") + } } /// Sum of all unitigs.bin sizes across all layers of partition `i` in `src`. @@ -354,8 +421,12 @@ fn partition_unitig_bytes(src: &KmerIndex, i: usize) -> u64 { let mut total = 0u64; for l in 0.. { let p = src.layer_unitigs_path(i, l); - if !p.exists() { break; } - if let Ok(m) = std::fs::metadata(&p) { total += m.len(); } + if !p.exists() { + break; + } + if let Ok(m) = std::fs::metadata(&p) { + total += m.len(); + } } total } @@ -382,7 +453,10 @@ fn compute_labels( }; *count += 1; labels.push(new_label.clone()); - all_genomes.push(GenomeInfo { label: new_label, meta: genome.meta.clone() }); + all_genomes.push(GenomeInfo { + label: new_label, + meta: genome.meta.clone(), + }); } source_labels.push(labels); } @@ -425,9 +499,9 @@ fn remove_dirs_named(root: &Path, name: &str) -> io::Result<()> { fn format_evidence(ev: &IndexMode) -> String { match ev { - IndexMode::Exact => "exact".to_string(), - IndexMode::Approx { b, z } => format!("approx (b={b}, z={z})"), - IndexMode::Hybrid { b, z } => format!("hybrid (b={b}, z={z})"), + IndexMode::Exact => "exact".to_string(), + IndexMode::Approx { b, z } => format!("approx (b={b}, z={z})"), + IndexMode::Hybrid { b, z } => format!("hybrid (b={b}, z={z})"), } } @@ -443,13 +517,21 @@ fn index_unitig_size(src: &KmerIndex) -> u64 { fn choose_base(sources: &[&KmerIndex], mode: MergeMode) -> usize { let needs_approx = sources.iter().any(|src| { !is_trivial(src, mode) - && matches!(src.meta.config.evidence, IndexMode::Approx { .. } | IndexMode::Hybrid { .. }) + && matches!( + src.meta.config.evidence, + IndexMode::Approx { .. } | IndexMode::Hybrid { .. } + ) }); - sources.iter().enumerate() + sources + .iter() + .enumerate() .filter(|(_, src)| { !needs_approx - || matches!(src.meta.config.evidence, IndexMode::Approx { .. } | IndexMode::Hybrid { .. }) + || matches!( + src.meta.config.evidence, + IndexMode::Approx { .. } | IndexMode::Hybrid { .. } + ) }) .max_by_key(|(_, src)| index_unitig_size(src)) .map(|(i, _)| i)