mecfs_bio.build_system.runner.gc_post_execute_hook

Post-execute hook that runs Python's cyclic garbage collector between tasks.

Long-running gwaslab pipelines accumulate cycle-held objects (Sumstats/LDSC internals) that refcounting alone cannot reclaim. Forcing a gc.collect() after each task reclaims multi-GB of resident memory per cell-analysis task in the s-LDSC system test.

Functions:

• gc_collect_post_execute_hook –

Attributes:

• logger –

logger module-attribute

logger = get_logger()

gc_collect_post_execute_hook

gc_collect_post_execute_hook(task: Task) -> None

Source code in mecfs_bio/build_system/runner/gc_post_execute_hook.py

def gc_collect_post_execute_hook(task: Task) -> None:
    rss_before_kb = _current_rss_kb()
    collected = gc.collect()
    rss_after_kb = _current_rss_kb()
    logger.debug(
        f"post-task gc.collect for {task.asset_id}: "
        f"unreachable_collected={collected} "
        f"rss_before_kb={rss_before_kb} rss_after_kb={rss_after_kb}"
    )