Merge pull request 'feat: add pipeline concurrency throttling and HPC build docs' (#30) from push-owwylwtskwzw into main

Reviewed-on: #30

docmd/installation.md

@@ -53,6 +53,22 @@ cargo build --release
 
 The compiled binary is at `target/release/obikmer`.
 
+### Building on HPC clusters (network filesystems)
+
+HPC home directories are typically on a network filesystem (Lustre, NFS) optimised for large sequential reads — not for the thousands of small file operations that Cargo generates during compilation. Building directly on such a filesystem can be extremely slow (0.1% CPU utilisation, tens of minutes for what should take seconds).
+
+**Always redirect the build directory to a local scratch disk:**
+
+```bash
+CARGO_TARGET_DIR=/scratch/local/$USER/cargo-target cargo build --release
+```
+
+Adapt the path to the local scratch available on your cluster (`/var/tmp`, `/tmp`, `/scratch/local`, etc.). Once built, copy the binary to a permanent location:
+
+```bash
+cp /scratch/local/$USER/cargo-target/release/obikmer ~/bin/
+```
+
 ## NUMA support
 
 NUMA-aware thread placement is active automatically on multi-socket Linux machines (detected at runtime via hwloc). No special build flag is required — the detection is built in and falls back gracefully to the single-pool adaptive strategy on:

src/obikmer/src/cli.rs

@@ -1,9 +1,9 @@
 use std::path::PathBuf;
-use std::sync::{Arc, Condvar, Mutex};
 
 use clap::Args;
 use obiread::NucPage;
 use obikseq::RoutableSuperKmer;
+use obipipeline::Throttled;
 
 // ── Shared arguments ──────────────────────────────────────────────────────────
 
@@ -103,54 +103,10 @@ impl CommonArgs {
     }
 }
 
-// ── Open-file throttling ──────────────────────────────────────────────────────
-
-struct FileSlots {
-    count:   Mutex<usize>,
-    condvar: Condvar,
-    max:     usize,
-}
-
-impl FileSlots {
-    fn new(max: usize) -> Self {
-        Self { count: Mutex::new(0), condvar: Condvar::new(), max }
-    }
-
-    fn acquire(&self) {
-        let mut count = self.count.lock().unwrap();
-        while *count >= self.max {
-            count = self.condvar.wait(count).unwrap();
-        }
-        *count += 1;
-    }
-
-    fn release(&self) {
-        let mut count = self.count.lock().unwrap();
-        *count -= 1;
-        self.condvar.notify_one();
-    }
-}
-
-struct SlotsGuard(Arc<FileSlots>);
-
-impl Drop for SlotsGuard {
-    fn drop(&mut self) {
-        self.0.release();
-    }
-}
-
 // ── Pipeline data carrier ─────────────────────────────────────────────────────
 
-/// A path bundled with an opaque guard token.
-/// The guard is acquired in the source thread and dropped by the flat worker
-/// once the file is fully read, releasing the open-file slot.
-pub struct PathWithSlot {
-    pub path:   PathBuf,
-    pub _guard: Box<dyn Send + 'static>,
-}
-
 pub enum PipelineData {
-    Path(PathWithSlot),
+    Path(Throttled<PathBuf>),
     NucPage(NucPage),
     Batch(Vec<RoutableSuperKmer>),
 }
@@ -158,20 +114,3 @@ pub enum PipelineData {
 unsafe impl Send for PipelineData {}
 unsafe impl Sync for PipelineData {}
 
-/// Wrap a path iterator so that at most `max_open` files are open simultaneously.
-/// Acquisition happens in the caller's thread (the pipeline source thread),
-/// never inside a worker, preventing deadlocks.
-pub fn throttle_paths(
-    source: impl Iterator<Item = PathBuf> + Send + 'static,
-    max_open: usize,
-) -> impl Iterator<Item = PathWithSlot> + Send + 'static {
-    let slots = Arc::new(FileSlots::new(max_open));
-    source.map(move |path| {
-        slots.acquire();
-        PathWithSlot {
-            path,
-            _guard: Box::new(SlotsGuard(Arc::clone(&slots))),
-        }
-    })
-}
-

src/obikmer/src/cmd/superkmer.rs

@@ -1,10 +1,13 @@
 use std::io::{self, BufWriter, Write};
+use std::path::PathBuf;
 
 use clap::Args;
 use obifastwrite::write_scatter;
 use obikseq::{RoutableSuperKmer, set_k, set_m};
 
-use crate::cli::{CommonArgs, PipelineData, PathWithSlot, partitions_to_bits, throttle_paths};
+use obipipeline::{Throttled, throttle};
+
+use crate::cli::{CommonArgs, PipelineData, partitions_to_bits};
 
 #[derive(Args)]
 pub struct SuperkmerArgs {
@@ -46,14 +49,15 @@ pub fn run(args: SuperkmerArgs) {
     set_k(k);
     set_m(m);
 
-    let path_source = throttle_paths(args.common.seqfile_paths(), max_open);
+    let path_source = throttle(args.common.seqfile_paths(), max_open);
 
     let pipe = obipipeline::make_pipe! {
-        PipelineData : PathWithSlot => Vec<RoutableSuperKmer>,
+        PipelineData : Throttled<PathBuf> => Vec<RoutableSuperKmer>,
         ||? {
             let k = k;
-            move |pw: PathWithSlot| {
-                let path_str = pw.path.to_str().unwrap_or("").to_owned();
+            move |pw: Throttled<PathBuf>| {
+                let path_str = pw.item.to_str().unwrap_or("").to_owned();
+                let _guard = pw.guard;
                 obiread::open_nuc_stream(&path_str, k)
             }
         } : Path => NucPage,

src/obikmer/src/steps/scatter.rs

@@ -6,16 +6,17 @@ use std::time::Instant;
 use obisys::spinner;
 use obiread::NucPage;
 use obikpartitionner::KmerPartition;
+use obipipeline::{ThrottleGuard, Throttled, throttle};
 use obisys::{Reporter, Stage};
 use tracing::info;
 
-use crate::cli::{PipelineData, PathWithSlot, throttle_paths};
+use crate::cli::PipelineData;
 
 // ── Iterator that keeps the slot guard alive until the file is exhausted ──────
 
 struct GuardedIter {
     inner:       Box<dyn Iterator<Item = NucPage> + Send>,
-    _guard:      Box<dyn Send + 'static>,
+    _guard:      ThrottleGuard,
     flat_active: Arc<AtomicU32>,
 }
 
@@ -49,7 +50,7 @@ pub fn scatter(
     use obikseq::RoutableSuperKmer;
 
     // Throttle in the source thread — never in a worker — to prevent deadlock.
-    let throttled = throttle_paths(path_source, max_open);
+    let throttled = throttle(path_source, max_open);
 
     let file_count      = Arc::new(AtomicU64::new(0));
     let flat_active     = Arc::new(AtomicU32::new(0));
@@ -57,19 +58,20 @@ pub fn scatter(
 
     let t = Stage::start("scatter");
     let pipe = obipipeline::make_pipe! {
-        PipelineData : PathWithSlot => Vec<RoutableSuperKmer>,
+        PipelineData : Throttled<PathBuf> => Vec<RoutableSuperKmer>,
         ||? {
             let file_count   = Arc::clone(&file_count);
             let flat_active  = Arc::clone(&flat_active);
             let k = k;
-            move |pw: PathWithSlot| {
-                let PathWithSlot { path, _guard } = pw;
+            move |pw: Throttled<PathBuf>| {
+                let path  = pw.item;
+                let guard = pw.guard;
                 let n = file_count.fetch_add(1, Ordering::Relaxed) + 1;
                 info!("indexing [{}]: {}", n, path.display());
                 let path_str = path.to_str().unwrap_or("").to_owned();
                 flat_active.fetch_add(1, Ordering::Relaxed);
                 obiread::open_nuc_stream(&path_str, k)
-                    .map(|iter| GuardedIter { inner: iter, _guard, flat_active: Arc::clone(&flat_active) })
+                    .map(|iter| GuardedIter { inner: iter, _guard: guard, flat_active: Arc::clone(&flat_active) })
             }
         } : Path => NucPage,
         | {

src/obikpartitionner/src/merge_layer.rs

@@ -6,6 +6,7 @@ use std::sync::{Arc, Mutex};
 use tracing::debug;
 use obipipeline::{
     Pipeline, PipelineError, PipelineSender, SharedFlatFn, Stage, WorkerPool,
+    ThrottleGuard, throttle,
     make_sink, make_source, make_transform,
 };
 
@@ -221,16 +222,18 @@ impl KmerPartition {
         debug!("partition {i}: de Bruijn graph build start — {n_src_layers} source layer(s)");
 
         enum Pass1Data {
-            File(PathBuf),
+            File((PathBuf, ThrottleGuard)),
             Batch(Vec<CanonicalKmer>),
             NewKmers(Vec<CanonicalKmer>),
         }
 
         const BATCH: usize = 4096;
-        // Inside pool.install() this returns the per-NUMA pool size; outside
-        // it returns the global pool size. Both are the right value here.
-        let n_workers = rayon::current_num_threads().max(1);
-        let capacity  = n_workers * 8;
+        let n_workers = rayon::current_num_threads().min(16).max(4);
+        let capacity  = 2;
+        // At most 2 files open simultaneously: keeps n_workers-2 workers free
+        // for the Transform stage. Each open file monopolises one worker for the
+        // full duration of its read, so this must stay well below n_workers.
+        let max_open  = 2;
 
         let dst_filter = Arc::clone(&dst_map);
         let g_shared   = Arc::new(Mutex::new(GraphDeBruijn::new()));
@@ -238,15 +241,18 @@ impl KmerPartition {
         let pass1_err: Arc<Mutex<Option<String>>> = Arc::new(Mutex::new(None));
         let err_cap    = Arc::clone(&pass1_err);
 
+        let throttled_paths = throttle(unitig_paths.into_iter(), max_open);
+
         let pipeline = Pipeline::new(
-            make_source!(Pass1Data, unitig_paths, File),
+            make_source!(Pass1Data, throttled_paths.map(|t| (t.item, t.guard)), File),
             vec![
                 Stage::Flat(Arc::new(
                     move |data: Pass1Data,
                           push:  &PipelineSender<Result<Pass1Data, PipelineError>>,
                           delta: &PipelineSender<isize>|
                     {
-                        if let Pass1Data::File(path) = data {
+                        if let Pass1Data::File((path, _guard)) = data {
+                            // _guard is dropped at end of this block, releasing the slot.
                             let reader = match UnitigFileReader::open_sequential(&path) {
                                 Ok(r)  => r,
                                 Err(e) => {
@@ -455,7 +461,7 @@ impl KmerPartition {
         }
 
         enum Pass2Data {
-            SrcLayer((usize, usize, PathBuf)),
+            SrcLayer((usize, usize, PathBuf, ThrottleGuard)),
             RawBatch((usize, usize, Arc<SrcLayerData>, Vec<CanonicalKmer>)),
             WriteBatch(Vec<(Option<usize>, usize, usize, u32)>),
         }
@@ -477,15 +483,21 @@ impl KmerPartition {
         let pass2_err: Arc<Mutex<Option<String>>> = Arc::new(Mutex::new(None));
         let err_cap2       = Arc::clone(&pass2_err);
 
+        let throttled_pass2 = throttle(pass2_items.into_iter(), max_open);
+
         let pipeline2 = Pipeline::new(
-            make_source!(Pass2Data, pass2_items, SrcLayer),
+            make_source!(Pass2Data, throttled_pass2.map(|t| {
+                let (col_offset, src_n, src_layer_dir) = t.item;
+                (col_offset, src_n, src_layer_dir, t.guard)
+            }), SrcLayer),
             vec![
                 Stage::Flat(Arc::new(
                     move |data: Pass2Data,
                           push:  &PipelineSender<Result<Pass2Data, PipelineError>>,
                           delta: &PipelineSender<isize>|
                     {
-                        if let Pass2Data::SrcLayer((col_offset, src_n, src_layer_dir)) = data {
+                        if let Pass2Data::SrcLayer((col_offset, src_n, src_layer_dir, _guard)) = data {
+                            // _guard dropped at end of block, releasing the slot.
                             let reader = match UnitigFileReader::open_sequential(
                                 &src_layer_dir.join("unitigs.bin"),
                             ) {

src/obipipeline/src/lib.rs

@@ -1,4 +1,5 @@
 mod scheduler;
+pub mod throttle;
 
 pub use scheduler::Pipe;
 pub use scheduler::PipeIter;
@@ -10,6 +11,10 @@ pub use scheduler::SinkFn;
 pub use scheduler::SourceFn;
 pub use scheduler::Stage;
 pub use scheduler::WorkerPool;
+pub use throttle::Throttle;
+pub use throttle::ThrottleGuard;
+pub use throttle::Throttled;
+pub use throttle::throttle;
 
 /// Re-export de `crossbeam_channel::Sender` utilisé dans les macros flat transform.
 /// Permet aux macros `make_flat_transform!` / `make_flat_transform_fallible!` d'utiliser

src/obipipeline/src/throttle.rs

@@ -0,0 +1,86 @@
+use std::sync::{Arc, Condvar, Mutex};
+
+// ── Throttle ──────────────────────────────────────────────────────────────────
+
+/// Counting semaphore: limits how many items from a source are in-flight
+/// simultaneously through the Flat stage of a pipeline.
+///
+/// Slots are acquired in the source thread before an item is emitted, and
+/// released when the corresponding `ThrottleGuard` is dropped (i.e. when the
+/// Flat worker finishes processing the item).  Acquisition must never happen
+/// inside a worker — only in the source thread — to prevent deadlocks.
+pub struct Throttle {
+    count:  Mutex<usize>,
+    condvar: Condvar,
+    max:    usize,
+}
+
+impl Throttle {
+    pub fn new(max: usize) -> Self {
+        Self { count: Mutex::new(0), condvar: Condvar::new(), max }
+    }
+
+    pub fn acquire(&self) {
+        let mut count = self.count.lock().unwrap();
+        while *count >= self.max {
+            count = self.condvar.wait(count).unwrap();
+        }
+        *count += 1;
+    }
+
+    fn release(&self) {
+        let mut count = self.count.lock().unwrap();
+        *count -= 1;
+        self.condvar.notify_one();
+    }
+}
+
+// ── ThrottleGuard ─────────────────────────────────────────────────────────────
+
+/// RAII guard: releases one slot in the `Throttle` when dropped.
+pub struct ThrottleGuard(Arc<Throttle>);
+
+impl Drop for ThrottleGuard {
+    fn drop(&mut self) {
+        self.0.release();
+    }
+}
+
+// ── Throttled<T> ──────────────────────────────────────────────────────────────
+
+/// An item paired with its throttle guard.
+///
+/// The guard keeps a slot acquired until this value is dropped.  In a Flat
+/// pipeline stage, carry the guard inside the worker closure until the item
+/// is fully processed, then let it drop.
+pub struct Throttled<T> {
+    pub item:  T,
+    pub guard: ThrottleGuard,
+}
+
+// ── throttle() ────────────────────────────────────────────────────────────────
+
+/// Wrap `source` so that at most `max_concurrent` items are emitted before
+/// earlier ones have been fully processed (i.e. their `ThrottleGuard` dropped).
+///
+/// Acquisition blocks the source thread until a slot is available.  This must
+/// be called in the source thread, never inside a pipeline worker.
+///
+/// # Example
+///
+/// ```ignore
+/// let throttled = obipipeline::throttle(file_paths, n_workers - 1);
+/// // Use `throttled` as the pipeline source; carry `item.guard` through the
+/// // Flat stage and let it drop when the file is fully read.
+/// ```
+pub fn throttle<I>(source: I, max_concurrent: usize) -> impl Iterator<Item = Throttled<I::Item>>
+where
+    I: Iterator,
+    I::Item: Send + 'static,
+{
+    let t = Arc::new(Throttle::new(max_concurrent));
+    source.map(move |item| {
+        t.acquire();
+        Throttled { item, guard: ThrottleGuard(Arc::clone(&t)) }
+    })
+}