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Segmentation Fault (core dumped) Error after installating into existing env

See original GitHub issue

🐛 Bug

After a fresh installation of aim onto 2 existing anaconda environments on my machine upon trying to use any command (e.g., aim version or aim init) I get Segmentation fault (core dumped) as an error.

To reproduce

$ pip install aim
...
$ aim version
Segmentation fault (core dumped)
$ aim
Segmentation fault (core dumped)
$ aim init
Segmentation fault (core dumped)

Expected behavior

I expect it to print a version like Aim v3.15.0 (for the version command) / not break on any basic command.

Environment

  • Aim Version (e.g., 3.0.1): 3.15.0 (also tried nightly, 3.16.0.dev20221128, same problem)
  • Python version: 3.9.13
  • pip version: 22.1.2
  • OS (e.g., Linux): Ubuntu 18.04.4 LTS (Bionic Beaver)
  • Any other relevant information:
    • I tested this on another Linux machine running Debian 11 (bullseye) in an anaconda environment and I had no problems there. Same Aim version, Python 3.8.13, pip 22.1.2.
    • I also created a new environment on the Ubuntu machine and installed aim and ran into no issues there (Python 3.9). So I believe this to be some sort of package error.

Additional context

Versions of required packages (from doing pip show aim which lists the required packages) in the broken environment.

aim-ui                        3.15.0
aimrecords                    0.0.7
aimrocks                      0.2.1
aiofiles                      22.1.0
alembic                       1.8.0
cachetools                    5.0.0
click                         8.1.3
click-default-group           1.2.2
cryptography                  37.0.2
fastapi                       0.67.0
filelock                      3.7.1
grpcio                        1.46.3
Jinja2                        3.1.2
numpy                         1.22.4
packaging                     20.9
Pillow                        9.1.1
protobuf                      3.20.1
psutil                        5.9.1
py3nvml                       0.2.7
python-dateutil               2.8.2
pytz                          2022.1
requests                      2.28.1
requests-oauthlib             1.3.1
requests-toolbelt             0.9.1
RestrictedPython              6.0
SQLAlchemy                    1.4.39
tqdm                          4.64.0
uvicorn                       0.20.0

Here’s the install output in the existing environment:

pip install aim
Collecting aim
  Downloading aim-3.15.0-cp39-cp39-manylinux_2_24_x86_64.whl (5.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 72.1 MB/s eta 0:00:00
Requirement already satisfied: cachetools>=4.0.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (5.0.0)
Requirement already satisfied: SQLAlchemy>=1.4.1 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (1.4.39)
Requirement already satisfied: alembic>=1.4.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (1.8.0)
Requirement already satisfied: filelock>=3.3.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (3.7.1)
Requirement already satisfied: Pillow>=8.0.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (9.1.1)
Requirement already satisfied: numpy>=1.12.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (1.22.4)
Requirement already satisfied: python-dateutil in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (2.8.2)
Requirement already satisfied: click>=7.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (8.1.3)
Requirement already satisfied: psutil>=5.6.7 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (5.9.1)
Collecting RestrictedPython>=5.1
  Downloading RestrictedPython-6.0-py3-none-any.whl (25 kB)
Requirement already satisfied: tqdm>=4.20.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (4.64.0)
Requirement already satisfied: jinja2>=2.10.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (3.1.2)
Collecting aim-ui==3.15.0
  Downloading aim-ui-3.15.0.tar.gz (19.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.0/19.0 MB 65.5 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Requirement already satisfied: cryptography>=3.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (37.0.2)
Requirement already satisfied: protobuf<4.0.0,>=3.9.2 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (3.20.1)
Collecting fastapi<0.68.0,>=0.65.0
  Downloading fastapi-0.67.0-py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.6/51.6 kB 5.1 MB/s eta 0:00:00
Requirement already satisfied: grpcio>=1.42.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (1.46.3)
Collecting aiofiles>=0.5.0
  Downloading aiofiles-22.1.0-py3-none-any.whl (14 kB)
Requirement already satisfied: pytz>=2019.1 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (2022.1)
Collecting aimrecords==0.0.7
  Downloading aimrecords-0.0.7-py2.py3-none-any.whl (28 kB)
Collecting uvicorn>=0.12.0
  Downloading uvicorn-0.20.0-py3-none-any.whl (56 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.9/56.9 kB 10.8 MB/s eta 0:00:00
Collecting aimrocks==0.2.1
  Downloading aimrocks-0.2.1-cp39-cp39-manylinux_2_24_x86_64.whl (6.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.1/6.1 MB 74.7 MB/s eta 0:00:00
Requirement already satisfied: packaging>=15.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (20.9)
Collecting py3nvml>=0.2.5
  Downloading py3nvml-0.2.7-py3-none-any.whl (55 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.5/55.5 kB 8.3 MB/s eta 0:00:00
Requirement already satisfied: requests in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from aim) (2.28.1)
Collecting base58==2.0.1
  Downloading base58-2.0.1-py3-none-any.whl (4.3 kB)
Requirement already satisfied: Mako in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from alembic>=1.4.0->aim) (1.2.0)
Requirement already satisfied: cffi>=1.12 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from cryptography>=3.0->aim) (1.15.0)
Collecting starlette==0.14.2
  Downloading starlette-0.14.2-py3-none-any.whl (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 10.5 MB/s eta 0:00:00
Requirement already satisfied: pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from fastapi<0.68.0,>=0.65.0->aim) (1.9.1)
Requirement already satisfied: six>=1.5.2 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from grpcio>=1.42.0->aim) (1.16.0)
Requirement already satisfied: MarkupSafe>=2.0 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from jinja2>=2.10.0->aim) (2.1.1)
Requirement already satisfied: pyparsing>=2.0.2 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from packaging>=15.0->aim) (3.0.9)
Collecting xmltodict
  Downloading xmltodict-0.13.0-py2.py3-none-any.whl (10.0 kB)
Requirement already satisfied: greenlet!=0.4.17 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from SQLAlchemy>=1.4.1->aim) (1.1.2)
Collecting h11>=0.8
  Downloading h11-0.14.0-py3-none-any.whl (58 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.3/58.3 kB 10.2 MB/s eta 0:00:00
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from requests->aim) (1.26.9)
Requirement already satisfied: certifi>=2017.4.17 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from requests->aim) (2022.9.24)
Requirement already satisfied: idna<4,>=2.5 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from requests->aim) (3.3)
Requirement already satisfied: charset-normalizer<3,>=2 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from requests->aim) (2.1.0)
Requirement already satisfied: pycparser in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from cffi>=1.12->cryptography>=3.0->aim) (2.21)
Requirement already satisfied: typing-extensions>=3.7.4.3 in /home/davina/mambaforge/envs/crrt/lib/python3.9/site-packages (from pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2->fastapi<0.68.0,>=0.65.0->aim) (4.2.0)
Building wheels for collected packages: aim-ui
  Building wheel for aim-ui (setup.py) ... done
  Created wheel for aim-ui: filename=aim_ui-3.15.0-py3-none-any.whl size=19166467 sha256=7bf09b45c851468631b2cf241f4b82773014ca1db930fb600ddb20ebf8162e42
  Stored in directory: /home/davina/.cache/pip/wheels/5f/26/08/0692fbd50918b088473d198e93c5bb30a47fc208aebe04a6a6
Successfully built aim-ui
Installing collected packages: aimrocks, aim-ui, xmltodict, starlette, RestrictedPython, h11, base58, aiofiles, uvicorn, py3nvml, fastapi, aimrecords, aim
Successfully installed RestrictedPython-6.0 aim-3.15.0 aim-ui-3.15.0 aimrecords-0.0.7 aimrocks-0.2.1 aiofiles-22.1.0 base58-2.0.1 fastapi-0.67.0 h11-0.14.0 py3nvml-0.2.7 starlette-0.14.2 uvicorn-0.20.0 xmltodict-0.13.0

Versions of required packages (from doing pip show aim which lists the required packages) in the fresh/working environment.

aim-ui             3.15.0
aimrecords         0.0.7
aimrocks           0.2.1
aiofiles           22.1.0
alembic            1.8.1
cachetools         5.2.0
click              8.1.3
cryptography       38.0.4
fastapi            0.67.0
filelock           3.8.0
grpcio             1.50.0
Jinja2             3.1.2
numpy              1.23.5
packaging          21.3
Pillow             9.3.0
protobuf           3.20.3
psutil             5.9.4
py3nvml            0.2.7
python-dateutil    2.8.2
pytz               2022.6
requests           2.28.1
RestrictedPython   6.0
SQLAlchemy         1.4.44
tqdm               4.64.1
uvicorn            0.20.0

Here is the output for an install in a fresh environment:

$ pip install aim
Collecting aim
  Using cached aim-3.15.0-cp39-cp39-manylinux_2_24_x86_64.whl (5.5 MB)
Collecting cachetools>=4.0.0
  Downloading cachetools-5.2.0-py3-none-any.whl (9.3 kB)
Collecting jinja2>=2.10.0
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 6.6 MB/s eta 0:00:00
Collecting uvicorn>=0.12.0
  Using cached uvicorn-0.20.0-py3-none-any.whl (56 kB)
Collecting numpy>=1.12.0
  Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 70.2 MB/s eta 0:00:00
Collecting Pillow>=8.0.0
  Downloading Pillow-9.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 74.5 MB/s eta 0:00:00
Collecting SQLAlchemy>=1.4.1
  Downloading SQLAlchemy-1.4.44-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 65.9 MB/s eta 0:00:00
Collecting psutil>=5.6.7
  Downloading psutil-5.9.4-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (280 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 280.2/280.2 kB 33.2 MB/s eta 0:00:00
Collecting click>=7.0
  Downloading click-8.1.3-py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.6/96.6 kB 5.4 MB/s eta 0:00:00
Collecting fastapi<0.68.0,>=0.65.0
  Using cached fastapi-0.67.0-py3-none-any.whl (51 kB)
Collecting aimrecords==0.0.7
  Using cached aimrecords-0.0.7-py2.py3-none-any.whl (28 kB)
Collecting filelock>=3.3.0
  Downloading filelock-3.8.0-py3-none-any.whl (10 kB)
Collecting requests
  Downloading requests-2.28.1-py3-none-any.whl (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 12.6 MB/s eta 0:00:00
Collecting grpcio>=1.42.0
  Downloading grpcio-1.50.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 72.0 MB/s eta 0:00:00
Collecting pytz>=2019.1
  Downloading pytz-2022.6-py2.py3-none-any.whl (498 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 498.1/498.1 kB 65.0 MB/s eta 0:00:00
Collecting aim-ui==3.15.0
  Using cached aim-ui-3.15.0.tar.gz (19.0 MB)
  Preparing metadata (setup.py) ... done
Collecting protobuf<4.0.0,>=3.9.2
  Downloading protobuf-3.20.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 67.7 MB/s eta 0:00:00
Collecting aimrocks==0.2.1
  Using cached aimrocks-0.2.1-cp39-cp39-manylinux_2_24_x86_64.whl (6.1 MB)
Collecting cryptography>=3.0
  Downloading cryptography-38.0.4-cp36-abi3-manylinux_2_24_x86_64.whl (4.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.0/4.0 MB 76.2 MB/s eta 0:00:00
Collecting RestrictedPython>=5.1
  Using cached RestrictedPython-6.0-py3-none-any.whl (25 kB)
Collecting aiofiles>=0.5.0
  Using cached aiofiles-22.1.0-py3-none-any.whl (14 kB)
Collecting packaging>=15.0
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 7.3 MB/s eta 0:00:00
Collecting python-dateutil
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 31.0 MB/s eta 0:00:00
Collecting alembic>=1.4.0
  Downloading alembic-1.8.1-py3-none-any.whl (209 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 209.8/209.8 kB 28.7 MB/s eta 0:00:00
Collecting tqdm>=4.20.0
  Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 7.6 MB/s eta 0:00:00
Collecting py3nvml>=0.2.5
  Using cached py3nvml-0.2.7-py3-none-any.whl (55 kB)
Collecting base58==2.0.1
  Using cached base58-2.0.1-py3-none-any.whl (4.3 kB)
Collecting Mako
  Downloading Mako-1.2.4-py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.7/78.7 kB 8.8 MB/s eta 0:00:00
Collecting cffi>=1.12
  Downloading cffi-1.15.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (441 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 441.2/441.2 kB 37.3 MB/s eta 0:00:00
Collecting pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2
  Downloading pydantic-1.10.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.2/13.2 MB 70.0 MB/s eta 0:00:00
Collecting starlette==0.14.2
  Using cached starlette-0.14.2-py3-none-any.whl (60 kB)
Collecting six>=1.5.2
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting pyparsing!=3.0.5,>=2.0.2
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Collecting xmltodict
  Using cached xmltodict-0.13.0-py2.py3-none-any.whl (10.0 kB)
Collecting greenlet!=0.4.17
  Downloading greenlet-2.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (535 kB)
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Collecting h11>=0.8
  Using cached h11-0.14.0-py3-none-any.whl (58 kB)
Collecting charset-normalizer<3,>=2
  Downloading charset_normalizer-2.1.1-py3-none-any.whl (39 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.13-py2.py3-none-any.whl (140 kB)
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Collecting idna<4,>=2.5
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Collecting certifi>=2017.4.17
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Collecting pycparser
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Collecting typing-extensions>=4.1.0
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Building wheels for collected packages: aim-ui
  Building wheel for aim-ui (setup.py) ... done
  Created wheel for aim-ui: filename=aim_ui-3.15.0-py3-none-any.whl size=19166430 sha256=f7c9981739beb6f2db04a83878d4c4416c7a7156f507662e45fac4cecfd1f51f
  Stored in directory: /home/davina/.cache/pip/wheels/ab/bb/23/929b12eba246778b24e1433d67060358e5c9896d26b39b7bef
Successfully built aim-ui
Installing collected packages: pytz, aimrocks, aim-ui, xmltodict, urllib3, typing-extensions, tqdm, starlette, six, RestrictedPython, pyparsing, pycparser, psutil, protobuf, Pillow, numpy, MarkupSafe, idna, h11, greenlet, filelock, click, charset-normalizer, certifi, cachetools, base58, aiofiles, uvicorn, SQLAlchemy, requests, python-dateutil, pydantic, py3nvml, packaging, Mako, jinja2, grpcio, cffi, aimrecords, fastapi, cryptography, alembic, aim
Successfully installed Mako-1.2.4 MarkupSafe-2.1.1 Pillow-9.3.0 RestrictedPython-6.0 SQLAlchemy-1.4.44 aim-3.15.0 aim-ui-3.15.0 aimrecords-0.0.7 aimrocks-0.2.1 aiofiles-22.1.0 alembic-1.8.1 base58-2.0.1 cachetools-5.2.0 certifi-2022.9.24 cffi-1.15.1 charset-normalizer-2.1.1 click-8.1.3 cryptography-38.0.4 fastapi-0.67.0 filelock-3.8.0 greenlet-2.0.1 grpcio-1.50.0 h11-0.14.0 idna-3.4 jinja2-3.1.2 numpy-1.23.5 packaging-21.3 protobuf-3.20.3 psutil-5.9.4 py3nvml-0.2.7 pycparser-2.21 pydantic-1.10.2 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2022.6 requests-2.28.1 six-1.16.0 starlette-0.14.2 tqdm-4.64.1 typing-extensions-4.4.0 urllib3-1.26.13 uvicorn-0.20.0 xmltodict-0.13.0

Environment diff: image

Issue Analytics

  • State:open
  • Created 10 months ago
  • Comments:8 (5 by maintainers)

github_iconTop GitHub Comments

2reactions
davzamancommented, Nov 29, 2022

Hi @SGevorg . Versions 3.13 and 3.14 break (segfault), however, 3.12 works. I also checked 3.11 and that works as well.

The only interesting thing I noticed was this error when I installed 3.12:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
pytorch-lightning 1.5.10 requires pyDeprecate==0.3.1, but you have pydeprecate 0.3.2 which is incompatible.
1reaction
alberttorosyancommented, Dec 9, 2022

@davzaman , thanks for additional info! This really helps to narrow the search area and find the cause of the issue.

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