concurrent.futures._base.TimeoutError

Start with src/utils/misc/process.py at mp_with_timeout and then inspect datasets/rcsb/process_mmcif_metadata.py where it is called. Reproduce the RCSB preprocessing timeout and determine how the failing sample should be reported; done means the original timeout is handled without the secondary IndexError and the problematic sample can be identified.

I encounter an issue, when I preprocess the rcsb data and run process_mmcif_metadata.py.
I don't know which sample has the problem, how to solve it? thanks!

Traceback (most recent call last):
  File "confdiff/ConfDiff/src/utils/misc/process.py", line 110, in mp_with_timeout
    result = next(result_itr)
  File "/home/ubuntu/anaconda3/envs/confdiff/lib/python3.9/site-packages/pebble/pool/base_pool.py", line 224, in next
    raise result
  File "/home/ubuntu/anaconda3/envs/confdiff/lib/python3.9/site-packages/pebble/pool/base_pool.py", line 264, in chunk_result
    return future.result(timeout=timeout)
  File "/home/ubuntu/anaconda3/envs/confdiff/lib/python3.9/concurrent/futures/_base.py", line 448, in result
    raise TimeoutError()
concurrent.futures._base.TimeoutError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/confdiff/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home/ubuntu/anaconda3/envs/confdiff/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "confdiff/ConfDiff/datasets/rcsb/process_mmcif_metadata.py", line 359, in <module>
    main(args)
  File "confdiff/ConfDiff/datasets/rcsb/process_mmcif_metadata.py", line 280, in main
    results = mp_with_timeout(
  File "confdiff/ConfDiff/src/utils/misc/process.py", line 117, in mp_with_timeout
    f"Timeout {error.args[1]} s: {error_report_fn(current_ix)}"
IndexError: tuple index out of range