Skip to content

fix: --runThreadN 1 ran on every core, not on one #166

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
BenjaminDEMAILLE wants to merge 2 commits into
base: main
Choose a base branch
from
Open

fix: --runThreadN 1 ran on every core, not on one #166

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ea56450
fix: --runThreadN 1 ran on every core, not on one
BenjaminDEMAILLE Jul 30, 2026
b391032
docs(changelog): record the --runThreadN 1 fix
BenjaminDEMAILLE Jul 30, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 5 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,11 @@ Sections commonly used: Features, Bug fixes, Other changes.

### Bug fixes

- `--runThreadN 1` ran on every logical core instead of on one. The
rayon pool was configured only above 1, and skipping it leaves rayon's
default of one worker per core. Output is unchanged; the run now uses
the thread count asked for.

- **STARsolo `Gene` assignment now requires exon concordance**, matching
STARsolo: a read counts toward a gene only when every aligned block
lies within the gene's exons, rather than merely overlapping one. This
Expand Down
12 changes: 7 additions & 5 deletions src/lib.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,11 +68,13 @@ pub fn run(params: &Parameters) -> anyhow::Result<()> {
// RSS for nothing. `build_global` errors if called twice; we
// ignore the error so the in-process tests that already
// initialised the pool still work.
if usize::from(params.run_thread_n) > 1 {
let _ = rayon::ThreadPoolBuilder::new()
.num_threads(params.run_thread_n.into())
.build_global();
}
//
// Configured at every value, `1` included. Skipping the build at 1 does not
// yield one thread: it leaves rayon's default of one worker per logical
// core, so `--runThreadN 1` ran on the whole machine.
let _ = rayon::ThreadPoolBuilder::new()
.num_threads(params.run_thread_n.into())
.build_global();

match params.run_mode {
RunMode::GenomeGenerate => genome_generate(params),
Expand Down
Loading