Hello,
I’m attempting to use the VoronoiFingerprint featurizer, but receiving a segfault. Other site featurizers such as the AGNI fingerprint are functioning fine for my data frame. See example code below.
----------Code----------
import numpy as np
import pandas as pd
import json
from pymatgen.core.structure import Structure
if name == “main”:
descriptor = ‘AGNI’
descriptor_settings = {‘cutoff’:4.0, ‘directions’:[None]}
descriptor = 'VoronoiFingerprint'
descriptor_settings = {'cutoff':6.5}
df = pd.read_json(‘dataframe.json’)
df.sort_index(inplace=True)
Structures are retrieved as dictionaries but can easily be converted to pymatgen.core.Structure objects as shown.
df[‘structure_pymatgen_object’] = pd.Series([Structure.from_dict(df[‘structure’][i]) for i in range(df.shape[0])], df.index)
if descriptor == ‘AGNI’:
from matminer.featurizers.site import AGNIFingerprints
AGNIFingerprints_featurizer = AGNIFingerprints(**descriptor_settings)
df = AGNIFingerprints_featurizer.featurize_dataframe(df, ['structure_pymatgen_object', 'site_index'])
if descriptor == ‘VoronoiFingerprint’:
from matminer.featurizers.site import VoronoiFingerprint
VoronoiFingerprint_featurizer = VoronoiFingerprint(**descriptor_settings)
VoronoiFingerprint_featurizer.set_n_jobs(1)
df = VoronoiFingerprint_featurizer.featurize_dataframe(df, ['structure_pymatgen_object', 'site_index'])
print(df.iloc[:,3:])
---------- End of Code -----------
---------Output---------------
VoronoiFingerprint: 0%| | 0/173 [00:00<?, ?it/s]
Segmentation fault: 11
----------- End of Output -----
Removing the “VoronoiFingerprint_featurizer.set_n_jobs(1)” will instead cause the progress bar to fill to 100%, but then hang indefinitely. Any idea what might be going wrong or advice to help debug this? I am running matminer 0.5.0 and anaconda’s python 3.6.4. Let me know if there’s any additional information I could send that would be helpful.
Thank you for your assistance!
Logan Williams