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Problem with layered and pattern fingerprints during parallel run [Windows] #113

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alkorolyov-selvita opened this issue Nov 26, 2024 · 0 comments
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@alkorolyov-selvita
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alkorolyov-selvita commented Nov 26, 2024

Is there an existing issue for this?

  • I have searched the existing issues and found nothing

Bug description

It seems that layered and pattern have default empty list [] param which fails to serialize during multiprocessing on windows.

How to reproduce the bug

import datamol as dm
from molfeat.trans import FPVecTransformer

trans = FPVecTransformer('pattern', n_jobs=-1, length=None)

df = dm.data.freesolv().iloc[:100]

trans(df.smiles).shape

Error messages and logs here please

Traceback (most recent call last):
  File "C:\Users\alexander.korolyov\miniforge3\envs\tadam\lib\site-packages\joblib\externals\loky\process_executor.py", line 426, in _process_worker
    call_item = call_queue.get(block=True, timeout=timeout)
  File "C:\Users\alexander.korolyov\miniforge3\envs\tadam\lib\multiprocessing\queues.py", line 122, in get
    return _ForkingPickler.loads(res)
  File "C:\Users\alexander.korolyov\miniforge3\envs\tadam\lib\site-packages\molfeat\calc\fingerprints.py", line 344, in __setstate__
    self.params = {
  File "C:\Users\alexander.korolyov\miniforge3\envs\tadam\lib\site-packages\molfeat\calc\fingerprints.py", line 345, in <dictcomp>
    k: (v if v not in SERIALIZABLE_CLASSES else SERIALIZABLE_CLASSES[v]())
TypeError: unhashable type: 'list'

BrokenProcessPool: A task has failed to un-serialize. Please ensure that the arguments of the function are all picklable.

Environment

Current environment
- Molfeat version: 0.10.1
- RDKit version:  2024.09.1
- OS : Windows 11
#- How you installed Molfeat (`conda`, `pip`, source):
conda
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