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fix: use mem::forget to avoid fjall Drop deadlock (#86) #87

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fix: use mem::forget to avoid fjall Drop deadlock (#86) #87

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12 changes: 6 additions & 6 deletions Cargo.lock
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20 changes: 12 additions & 8 deletions datafusion/bio-function-vep/src/cache_builder.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -901,6 +901,12 @@ impl CacheBuilder {
compact_start.elapsed().as_secs_f64()
);

// Skip fjall's Drop which deadlocks when background worker threads are busy
// compacting — the bounded(1000) flume channel fills up, send() blocks while
// the worker is still in compact(). All data is persisted and compacted above.
// See: https://github.com/biodatageeks/datafusion-bio-functions/issues/86
std::mem::forget(store);

let elapsed = start_time.elapsed().as_secs_f64();
info!(
"variation.fjall rebuilt: {} positions, {} variants, {:.1} MB in {:.1}s",
Expand Down Expand Up @@ -1434,14 +1440,12 @@ impl CacheBuilder {
db.persist(fjall::PersistMode::SyncAll)
.map_err(|e| DataFusionError::External(Box::new(e)))?;

info!("translation_sift.fjall: closing database...");
let close_start = Instant::now();
drop(sift_store);
drop(db);
info!(
"translation_sift.fjall: database closed in {:.1}s",
close_start.elapsed().as_secs_f64()
);
// Skip fjall's Drop which deadlocks when background worker threads are busy
// compacting — the bounded(1000) flume channel fills up, send() blocks while
// the worker is still in compact(). All data is persisted above.
// See: https://github.com/biodatageeks/datafusion-bio-functions/issues/86
std::mem::forget(sift_store);
std::mem::forget(db);

let elapsed = start_time.elapsed().as_secs_f64();
info!(
Expand Down
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