refactor: centralize CPU core detection using cgroup-aware utility

Introduce `obisys::effective_parallelism()` to read Linux cgroup v1/v2 CPU quotas from sysfs, preventing thread pool oversubscription in containerized environments. Replace direct `std::thread::available_parallelism()` calls across `obikindex` and `obikmer` with this centralized function. Bump `obikmer` version to 1.1.41.

.gitea/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: CI
+pname: CI
 
 on:
   pull_request:

src/Cargo.lock

@@ -1715,7 +1715,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.40"
+version = "1.1.41"
 dependencies = [
  "clap",
  "csv",

src/obikindex/src/numa.rs

@@ -79,9 +79,7 @@ pub fn build() -> NumaSetup {
     }
 
     // UMA fallback: single synthetic node, all cores, no pool, no pinning.
-    let n_cores = std::thread::available_parallelism()
+    let n_cores = obisys::effective_parallelism();
-        .map(|n| n.get())
-        .unwrap_or(1);
     debug!("UMA: single synthetic node, {} core(s)", n_cores);
     NumaSetup {
         pools: vec![None],
@@ -91,9 +89,7 @@ pub fn build() -> NumaSetup {
 
 #[cfg(not(feature = "numa"))]
 pub fn build() -> NumaSetup {
-    let n_cores = std::thread::available_parallelism()
+    let n_cores = obisys::effective_parallelism();
-        .map(|n| n.get())
-        .unwrap_or(1);
     debug!("UMA: single synthetic node, {} core(s)", n_cores);
     NumaSetup {
         pools: vec![None],

src/obikindex/src/siblings.rs

@@ -350,7 +350,7 @@ impl KmerIndex {
         // every single variant — fine at the scale of a handful of test
         // k-mers, but with billions of lookups against a real index this
         // manifested as ~90% system time, observed in practice. ───────────
-        let n_workers = std::thread::available_parallelism().map(|n| n.get()).unwrap_or(4);
+        let n_workers = obisys::effective_parallelism();
         let capacity = 256;
 
         // Throttling is not optional once a `Flat` stage is in the pipeline

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.40"
+version = "1.1.41"
 edition = "2024"
 
 [[bin]]

src/obikmer/src/cli.rs

@@ -38,9 +38,7 @@ pub struct CommonArgs {
     #[arg(
         short = 'T',
         long,
-        default_value_t = std::thread::available_parallelism()
+        default_value_t = obisys::effective_parallelism()
-            .map(|n| n.get())
-            .unwrap_or(1)
     )]
     pub threads: usize,
 

src/obikmer/src/cmd/query.rs

@@ -70,9 +70,7 @@ pub struct QueryArgs {
     #[arg(
         short = 'T',
         long,
-        default_value_t = std::thread::available_parallelism()
+        default_value_t = obisys::effective_parallelism()
-            .map(|n| n.get())
-            .unwrap_or(1)
     )]
     pub threads: usize,
 

src/obisys/src/lib.rs

@@ -202,6 +202,94 @@ fn cgroup_v1_available() -> Option<u64> {
     Some(limit.saturating_sub(used))
 }
 
+// ── CPU parallelism query ────────────────────────────────────────────────────
+
+/// Returns the number of cores this process can actually use concurrently.
+///
+/// `std::thread::available_parallelism()` reads CPU affinity
+/// (`sched_getaffinity`), not the container's CPU quota — a Docker/cgroup
+/// container commonly reports the *host's* full core count this way while
+/// actually being throttled (via `cpu.max`/`cpu.cfs_quota_us`) to a fraction
+/// of a core. Sizing a thread/worker pool off the unthrottled count causes
+/// severe oversubscription: dozens of threads contending for a sliver of
+/// real CPU time, which can look indistinguishable from a hang for minutes
+/// or hours (observed in CI). On Linux, this reads the cgroup CPU quota
+/// first and returns `min(cgroup_quota, host_parallelism)` when a finite
+/// quota is found; falls back to `available_parallelism()` otherwise (same
+/// convention as [`available_memory_bytes`]).
+pub fn effective_parallelism() -> usize {
+    let host = std::thread::available_parallelism().map(|n| n.get()).unwrap_or(1);
+    #[cfg(target_os = "linux")]
+    {
+        if let Some(quota) = cgroup_v2_cpu_quota() {
+            let effective = quota.clamp(1, host);
+            tracing::debug!(host, quota, effective, source = "cgroup v2", "effective_parallelism");
+            return effective;
+        }
+        if let Some(quota) = cgroup_v1_cpu_quota() {
+            let effective = quota.clamp(1, host);
+            tracing::debug!(host, quota, effective, source = "cgroup v1", "effective_parallelism");
+            return effective;
+        }
+    }
+    tracing::debug!(host, effective = host, source = "available_parallelism (no cgroup quota found)", "effective_parallelism");
+    host
+}
+
+/// cgroup v2 (unified hierarchy): reads `cpu.max` ("<quota> <period>", or
+/// "max <period>" when unlimited) for the current process's cgroup, rounded
+/// up to whole cores. Returns `None` if unlimited or on any parse error.
+#[cfg(target_os = "linux")]
+fn cgroup_v2_cpu_quota() -> Option<usize> {
+    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
+    let rel = cgroup
+        .lines()
+        .find(|l| l.starts_with("0::"))?
+        .strip_prefix("0::")?
+        .trim();
+    let base = format!("/sys/fs/cgroup{rel}");
+    let raw = std::fs::read_to_string(format!("{base}/cpu.max")).ok()?;
+    let mut parts = raw.split_whitespace();
+    let quota_str = parts.next()?;
+    let period: f64 = parts.next()?.parse().ok()?;
+    if quota_str == "max" {
+        return None; // unlimited
+    }
+    let quota: f64 = quota_str.parse().ok()?;
+    Some((quota / period).ceil().max(1.0) as usize)
+}
+
+/// cgroup v1 (cpu subsystem): reads `cpu.cfs_quota_us`/`cpu.cfs_period_us`,
+/// rounded up to whole cores. Returns `None` if unlimited (quota <= 0) or on
+/// any parse error.
+#[cfg(target_os = "linux")]
+fn cgroup_v1_cpu_quota() -> Option<usize> {
+    let cgroup = std::fs::read_to_string("/proc/self/cgroup").ok()?;
+    let path = cgroup
+        .lines()
+        .find(|l| l.contains(":cpu:") || l.contains(":cpu,cpuacct:"))?
+        .split(':')
+        .nth(2)?;
+    let base = format!("/sys/fs/cgroup/cpu{path}");
+    let quota: i64 = std::fs::read_to_string(format!("{base}/cpu.cfs_quota_us"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    if quota <= 0 {
+        return None; // unlimited
+    }
+    let period: i64 = std::fs::read_to_string(format!("{base}/cpu.cfs_period_us"))
+        .ok()?
+        .trim()
+        .parse()
+        .ok()?;
+    if period <= 0 {
+        return None;
+    }
+    Some(((quota as f64) / (period as f64)).ceil().max(1.0) as usize)
+}
+
 // ── raw helpers ───────────────────────────────────────────────────────────────
 
 fn get_rusage() -> rusage {
@@ -654,9 +742,7 @@ impl fmt::Display for Reporter {
             return Ok(());
         }
 
-        let n_cores = std::thread::available_parallelism()
+        let n_cores = effective_parallelism();
-            .map(|n| n.get())
-            .unwrap_or(1);
 
         // column widths
         let nw = self