Open OmarAshkar opened 1 year ago
nanli-emory
commented
1 year ago Hi @OmarAshkar, could you provide more information about your run environments such as the version of OS, python, and docker? what GPUs do you use? It will help us to narrow down the issues. Thank you.
VolodymyrChapman
commented
11 months ago TL;DR Downgrade protobuf to 3.20.x or below
I recently built the environment from the CUDA 11 requirements.txt on Ubuntu 22.04 and this same step failed due to protobuf (cannot find the exact reason for the error now) but the associated guidance in the error was to downgrade protobuf to version <=3.20.x .
I performed:
$ pip install protobuf==3.20.0
After which, the environment worked in all functions (training model 0, embedding, superpixel generation and retraining of DL). My working environment:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.0.0 pypi_0 pypi
albumentations 0.4.3 pypi_0 pypi
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
cachetools 4.2.4 pypi_0 pypi
certifi 2023.7.22 pypi_0 pypi
chardet 4.0.0 pypi_0 pypi
click 8.1.7 pypi_0 pypi
config 0.4.2 pypi_0 pypi
contourpy 1.1.1 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
flask 1.1.2 pypi_0 pypi
flask-restless 0.17.0 pypi_0 pypi
flask-sqlalchemy 2.4.4 pypi_0 pypi
fonttools 4.43.1 pypi_0 pypi
google-auth 1.35.0 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
grpcio 1.59.0 pypi_0 pypi
idna 2.10 pypi_0 pypi
imageio 2.9.0 pypi_0 pypi
imgaug 0.2.6 pypi_0 pypi
importlib-metadata 6.8.0 pypi_0 pypi
importlib-resources 6.1.0 pypi_0 pypi
itsdangerous 1.1.0 pypi_0 pypi
jinja2 3.0.3 pypi_0 pypi
joblib 1.3.2 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_2 conda-forge
libgomp 13.2.0 h807b86a_2 conda-forge
libnsl 2.0.0 hd590300_1 conda-forge
libsqlite 3.43.2 h2797004_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
llvmlite 0.39.1 pypi_0 pypi
markdown 3.5 pypi_0 pypi
markupsafe 2.1.3 pypi_0 pypi
matplotlib 3.7.3 pypi_0 pypi
mimerender 0.6.0 pypi_0 pypi
ncurses 6.4 hcb278e6_0 conda-forge
networkx 3.1 pypi_0 pypi
numba 0.56.4 pypi_0 pypi
numpy 1.20.3 pypi_0 pypi
oauthlib 3.2.2 pypi_0 pypi
opencv-python-headless 4.5.3.56 pypi_0 pypi
openssl 3.1.3 hd590300_0 conda-forge
packaging 23.2 pypi_0 pypi
pillow 8.1.2 pypi_0 pypi
pip 23.2.1 pyhd8ed1ab_0 conda-forge
protobuf 3.20.0 pypi_0 pypi
pyasn1 0.5.0 pypi_0 pypi
pyasn1-modules 0.3.0 pypi_0 pypi
pynndescent 0.5.10 pypi_0 pypi
pyparsing 3.1.1 pypi_0 pypi
python 3.8.18 hd12c33a_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python-mimeparse 1.6.0 pypi_0 pypi
pywavelets 1.4.1 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
requests 2.25.1 pypi_0 pypi
requests-oauthlib 1.3.1 pypi_0 pypi
rsa 4.9 pypi_0 pypi
scikit-image 0.18.1 pypi_0 pypi
scikit-learn 0.24.0 pypi_0 pypi
scipy 1.6.0 pypi_0 pypi
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
sqlalchemy 1.3.22 pypi_0 pypi
tensorboard 2.4.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
threadpoolctl 3.2.0 pypi_0 pypi
tifffile 2023.7.10 pypi_0 pypi
tk 8.6.13 h2797004_0 conda-forge
torch 1.8.1+cu111 pypi_0 pypi
torchaudio 0.8.1 pypi_0 pypi
torchvision 0.9.1+cu111 pypi_0 pypi
ttach 0.0.2 pypi_0 pypi
typing-extensions 4.8.0 pypi_0 pypi
umap-learn 0.5.1 pypi_0 pypi
urllib3 1.26.17 pypi_0 pypi
werkzeug 2.0.3 pypi_0 pypi
wheel 0.41.2 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.17.0 pypi_0 pypi
Hello, I am trying to use the tool. I run "Make patches", but the next step fails with
I have build with docker container.
Any help is appreciated.
Best Regards, Omar