[BUG] ImportError: undefined symbol: _ZN3c104cuda20CUDACachingAllocator9allocatorE

[umutdundar99]

Describe the bug I use virtual environment and all my pytorch and cuda versions are compatible with FastGeodis. I downloaded FastGeodis with all three combination: -pip install FastGeodis -pip install git+https://github.com/masadcv/FastGeodis -pip install FastGeodis --no-build-isolation Important Note: I have tried to delete and create new virtual env or conda env. It did not solve my problem.

But, still I got this error: import FastGeodis File "/home/umut_dundar_smartalpha_ai/alpha_trainer/.venv/lib/python3.8/site-packages/FastGeodis/init.py", line 33, in import FastGeodisCpp ImportError: /home/umut_dundar_smartalpha_ai/alpha_trainer/.venv/lib/python3.8/site-packages/FastGeodisCpp.cpython-38-x86_64-linux-gnu.so: undefined symbol: _ZN3c104cuda20CUDACachingAllocator9allocatorE

It can not find the FastGeodisCpp file in FastGeodis library.

Expected behavior I want to know how can I fix it.

Desktop (please complete the following information):

• Ubuntu 22.04
• aiohttp 3.8.4

CUDA VERSION == 11.8.0 efficientnet-pytorch 0.7.1
FastGeodis 1.0.3
filelock 3.12.0
flatbuffers 23.5.26
flatten-dict 0.4.2
flufl.lock 7.1.1
frozenlist 1.3.3
fsspec 2023.5.0
funcy 2.0
gitdb 4.0.10
GitPython 3.1.31
google-api-core 2.11.0
google-auth 2.19.0
google-cloud-core 2.3.2
google-cloud-storage 2.9.0
google-crc32c 1.5.0
google-resumable-media 2.5.0
googleapis-common-protos 1.59.0
grandalf 0.8
huggingface-hub 0.14.1
humanfriendly 10.0
hydra-colorlog 1.2.0
hydra-core 1.3.2
idna 3.4
imageio 2.30.0
importlib-resources 5.12.0
iterative-stratification 0.1.7
iterative-telemetry 0.0.8
joblib 1.2.0
kombu 5.2.4
kornia 0.6.12
lazy-loader 0.2
lightning-utilities 0.8.0
markdown-it-py 2.2.0
mdurl 0.1.2
mpmath 1.3.0
multidict 6.0.4
munch 3.0.0
nanotime 0.5.2
networkx 3.1
numpy 1.24.3
omegaconf 2.3.0
onnx 1.14.0
onnxruntime 1.15.0
onnxsim 0.4.28
opencv-python-headless 4.7.0.72
orjson 3.8.14
packaging 23.1
pandas 2.0.2
pathspec 0.11.1
pathtools 0.1.2
Pillow 9.5.0
pip 20.0.2
pkg-resources 0.0.0
platformdirs 3.5.1
pretrainedmodels 0.7.4
prompt-toolkit 3.0.38
protobuf 4.23.2
psutil 5.9.5
pyasn1 0.5.0
pyasn1-modules 0.3.0
pycparser 2.21
pydot 1.4.2
pygit2 1.12.1
Pygments 2.15.1
pygtrie 2.5.0
pyparsing 3.0.9
python-dateutil 2.8.2
pytorch-lightning 1.9.5
pytorch-ranger 0.1.1
pytz 2023.3
PyWavelets 1.4.1
PyYAML 6.0
qudida 0.0.4
regex 2023.5.5
requests 2.31.0
rich 13.4.1
rsa 4.9
ruamel.yaml 0.17.31
ruamel.yaml.clib 0.2.7
safetensors 0.3.1
scikit-image 0.20.0
scikit-learn 1.2.2
scipy 1.10.1
scmrepo 1.0.3
segmentation-models-pytorch 0.3.3
sentry-sdk 1.24.0
setproctitle 1.3.2
setuptools 44.0.0
shortuuid 1.0.11
shtab 1.6.1
six 1.16.0
smmap 5.0.0
sqltrie 0.3.1
sympy 1.12
tabulate 0.9.0
threadpoolctl 3.1.0
tifffile 2023.4.12
timm 0.9.2
tokenizers 0.13.3
tomlkit 0.11.8
torch 1.13.1+cu117 torch-optimizer 0.3.0
torchmetrics 0.11.0
torchvision 0.14.1+cu117 tqdm 4.65.0
transformers 4.29.2

[masadcv]

Hi, Similar issue was reported earlier here: https://github.com/masadcv/FastGeodis/issues/39 - can you try debugging using information there. It seemed to have fixed with fresh venv/python3.9 venv.

In case it still does not work, can you follow the steps here to try manual compile and paste the output here as a comment: https://github.com/masadcv/FastGeodis/issues/35#issuecomment-1247305033

[umutdundar99]

35 has solved the problem, thank you so much for quick respond!

[umutdundar99]

I built it successfully and I can import the FastGeodis now, but another error arises as i want to use the function of a library.

fg_dist = FastGeodis.generalised_geodesic2d(fg_mask, fg_mask, self.v, self.lamb, self.iterations) AttributeError: module 'FastGeodis' has no attribute 'generalised_geodesic2d'

I faced this error during the loss calculation.

[masadcv]

Seems like now you have a conflicting installation of the library.

Can you try again with a fresh virtualenv? If issues then report here with output of: pip list and the specific steps you followed to install/test

[masadcv]

Hi @umutdundar99 , Just checking, did you manage to solve this issues? If so, could you add a few lines how you did it so it may help anyone in future going through similar setup issues...

[umutdundar99]

Hi @masadcv , sorry for the late reply, I've fixed the issue recently. Deleting and reinstalling Cuda and using Python 3.8 solved my problem. Only Cuda 11.7 version worked for me. Thank you a lot for your help!

[masadcv]

Great! Many thanks for reporting... I am glad I could be of help here. I will close this issue now.