8000 mk_prepare_receptor.py fails if running multiple processes · Issue #351 · forlilab/Meeko · GitHub
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mk_prepare_receptor.py fails if running multiple processes #351
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mk_prepare_receptor.py fails if running multiple processes#351
@diogomart

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@diogomart
diogomart
opened on Apr 24, 2025

Reported by @pietscio and @nbruciaferri

The error is raised inside function update_H_positions in polymer.py. This check fails:

Meeko/meeko/polymer.py

Lines 448 to 451 in 07a38f8

if len(used_h) != len(to_del):
raise RuntimeError(
f"Updated {len(used_h)} H positions but deleted {len(to_del)}"
)

This never happens if there is only one process running. But happens quite frequently if multiple processes at the OS level (not python multiprocessing) are running simultaneously. Adding print statements for debugging purposes fixed the problem.

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