indigo_renderer segfault in multithreaded context (1.5.0)

[flc]

Hi,

The segmentation fault can be reproduced with the following code:

import concurrent.futures
import indigo
from indigo import renderer as indigo_renderer

SMILES_LIST = [
    'C',
    'CC',
    'CCC',
    'CCCCC',
    'CCCCCC',
    'CCCCCCC',
    'CCCCCCCC',
]

def render(smiles):
    ind = indigo.Indigo()
    imol = ind.loadMolecule(smiles)
    renderer = indigo_renderer.IndigoRenderer(ind)
    ind.setOption('render-output-format', 'png')
    buff = renderer.renderToBuffer(imol)
    return buff.tobytes()

with concurrent.futures.ThreadPoolExecutor(max_workers=2) as executor:
    futures_dict = {
        executor.submit(render, smiles): smiles
        for smiles in SMILES_LIST
    }
    for future in concurrent.futures.as_completed(futures_dict):
        smi = futures_dict[future]
        try:
            data = future.result()
        except Exception as exc:
            print(exc)
        else:
            print(data)

$ PYTHONFAULTHANDLER=1 python indigo_threading_test.py
Fatal Python error: Segmentation fault

Thread 0x00007fd2bbfff700 (most recent call first):
  File "/home/f/virtualenvs/so2/lib/python3.8/site-packages/indigo/renderer.py", line 77 in renderToBuffer
  File "indigo_threading_test.py", line 20 in render
  File "/usr/lib/python3.8/concurrent/futures/thread.py", line 57 in run
  File "/usr/lib/python3.8/concurrent/futures/thread.py", line 80 in _worker
  File "/usr/lib/python3.8/threading.py", line 870 in run
  File "/usr/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/lib/python3.8/threading.py", line 890 in _bootstrap

Current thread 0x00007fd2c0973700 (most recent call first):
  File "/home/f/.virtualenvs/so2/lib/python3.8/site-packages/indigo/renderer.py", line 77 in renderToBuffer
  File "indigo_threading_test.py", line 20 in render
  File "/usr/lib/python3.8/concurrent/futures/thread.py", line 57 in run
  File "/usr/lib/python3.8/concurrent/futures/thread.py", line 80 in _worker
  File "/usr/lib/python3.8/threading.py", line 870 in run
  File "/usr/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007fd2c275f740 (most recent call first):
  File "/usr/lib/python3.8/threading.py", line 302 in wait
  File "/usr/lib/python3.8/threading.py", line 558 in wait
  File "/usr/lib/python3.8/concurrent/futures/_base.py", line 244 in as_completed
  File "indigo_threading_test.py", line 28 in <module>
Segmentation fault

No segfault if:

• ThreadPoolExecutor.max_workers=1
• indigo 1.4.3 is used
• only Indigo is used and the IndigoRenderer is not used

The segfault still occurs if:

• global Indigo and/or IndigoRenderer instance is used and not initialized inside the function

Python version:
Python 3.8.11

Indigo version:
1.5.0-g1aef03cac-x86_64-linux-gnu-9.3.1

[even1024]

@flc , we are working on the issue. Will fix it soon.

[even1024]

Fixed with PR: #489

[mkviatkovskii]

Dear @flc,
We have fixed the problem. I'll inform you when new version with fix appears in public repositories. I expect it to happen before the end of the week.