SystemError: Bad call flags in PyCFunction_Call. METH_OLDARGS is no longer…

[Miro Moman]

Hello,

Running Gypsum-DL in parallel within Conda 4.8.3 (Python 3.6.10 :: Anaconda, Inc.) I receive the error message below. However, with a slightly older version the same dataset was running fine.

Contents of MolContainers
        MolContainer #0 (CHEMBL65794)
            Mol #0: CO/N=C(\C(=O)N[C@@H]1C(=O)N2C(C(=O)[O-])=C(C[n+]3cccc4c3CCC4
                )CS[C@H]12)c1csc(=N)[nH]1
            Mol #1: CO/N=C(C(\O)=N/[C@@H]1C(=O)N2C(C(=O)[O-])=C(C[n+]3cccc4c3CCC
                4)CS[C@H]12)/c1csc(N)n1
            Mol #2: CO/N=C(\C(=O)[N-][C@@H]1C(=O)N2C(C(=O)[O-])=C(C[n+]3cccc4c3C
                CC4)CS[C@H]12)c1csc(=N)[nH]1
            Mol #3: CO/N=C(\C(=O)[N-][C@@H]1C(O)=[N+]2C(C(=O)[O-])=C(C[n+]3cccc4
                c3CCC4)CS[C@H]12)c1csc(N)n1
            Mol #4: CO/N=C(\C(=O)N[C@@H]1C(O)=[N+]2C(C(=O)[O-])=C(C[n+]3cccc4c3C
                CC4)CS[C@H]12)c1csc(N)n1
Converting all molecules to 3D structures.
Generating several conformers of molecules with non-aromatic rings (boat vs.
    chair, etc.)...
Process Process-45:
Traceback (most recent call last):
  File "/home/mirix/miniconda3/envs/coronavirus/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/home/mirix/miniconda3/envs/coronavirus/lib/python3.6/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/home/mirix/home/qrl/coronavirus/gypsum_dl/gypsum_dl/Parallelizer.py", line 687, in worker
    result = func(*args)
  File "/home/mirix/home/qrl/coronavirus/gypsum_dl/gypsum_dl/Steps/ThreeD/GenerateAlternate3DNonaromaticRingConfs.py", line 267, in parallel_get_ring_confs
    groups = kmeans2(pts, num_clusters, minit="points")[1]
  File "/home/mirix/.local/lib/python3.6/site-packages/scipy/cluster/vq.py", line 702, in kmeans2
    code_book = init_meth(data, k)
  File "/home/mirix/.local/lib/python3.6/site-packages/scipy/cluster/vq.py", line 483, in _kpoints
    idx = np.random.choice(data.shape[0], size=k, replace=False)
SystemError: Bad call flags in PyCFunction_Call. METH_OLDARGS is no longer supported!
Segmentation fault (core dumped)

[Miro Moman]

NOTE: This was using the multiprocessor option. Only certain smiles fail. Now I am trying the mpi version, in which case I had to remove the –use_durrant_lab_filters option, otherwise all smiles failed.

[Jacob Durrant]

Hi Miro. Much thanks for your interest in Gypsum. This appears to be an error in the scipy or numpy libraries. Can you tell me which versions of those libraries you’re using? On my setup, I never see the error you mentioned:

Python 3.7.6 | packaged by conda-forge
numpy 1.18.5
scipy 1.4.1
rdkit 2020.03.1

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