pythoncronslurmmodulenotfounderrorcertifi

No module named certifi

When executing python3 (Python 3.6.8) script on a local directory, it works well, but when running sbatch job in slurm, complains about certifi.

python3 -m pip install certifi

Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: certifi in /usr/local/lib/python3.6/site-packages (2020.12.5)

After adding to the python code this:

import sys
import os
sys.path.append(os.getcwd())

or this:

import sys
import os
module_path = os.path.abspath(os.getcwd())

if module_path not in sys.path:

    sys.path.append(module_path)

the same error occurs. It seems that certifi is installed.

pip show certifi

Name: certifi
Version: 2020.12.5
Summary: Python package for providing Mozilla's CA Bundle.
Home-page: https://certifiio.readthedocs.io/en/latest/
Author: Kenneth Reitz
Author-email: me@kennethreitz.com
License: MPL-2.0
Location: /usr/local/lib/python3.6/site-packages
Requires:
Required-by: requests

The error after running python code (without having the line 'import certifi' in python code):

Traceback (most recent call last):
  File "/home/username/test/test.py", line 19, in <module>
    from textattack.augmentation import WordNetAugmenter, EmbeddingAugmenter, EasyDataAugmenter, CharSwapAugmenter
  File "/home/username/.local/lib/python3.6/site-packages/textattack/__init__.py", line 12, in <module>
    from . import (
  File "/home/username/.local/lib/python3.6/site-packages/textattack/attack_recipes/__init__.py", line 21, in <module>
    from .attack_recipe import AttackRecipe
  File "/home/username/.local/lib/python3.6/site-packages/textattack/attack_recipes/attack_recipe.py", line 9, in <module>
    from textattack.shared import Attack
  File "/home/username/.local/lib/python3.6/site-packages/textattack/shared/__init__.py", line 11, in <module>
    from . import utils
  File "/home/username/.local/lib/python3.6/site-packages/textattack/shared/utils/__init__.py", line 1, in <module>
    from .install import *
  File "/home/username/.local/lib/python3.6/site-packages/textattack/shared/utils/install.py", line 9, in <module>
    import requests
  File "/home/username/.local/lib/python3.6/site-packages/requests/__init__.py", line 118, in <module>
    from . import utils
  File "/home/username/.local/lib/python3.6/site-packages/requests/utils.py", line 25, in <module>
    from . import certs
  File "/home/username/.local/lib/python3.6/site-packages/requests/certs.py", line 15, in <module>
    from certifi import where
ModuleNotFoundError: No module named 'certifi'

The error (with having the line 'import certifi' in python code):

Traceback (most recent call last):
  File "/home/username/projecttest_LR_attack/LR_attack.py", line 17, in <module>
    import certifi
ModuleNotFoundError: No module named 'certifi'

What could be the solution to the issue?

Solution

  • Are the same modules installed on the compute nodes as locally? You may need to check with the Slurm admins.