Docker with Conda: GLIBCXX_3.4.29 not found, Libstdc++ Issues in Conda/PyTorch Environment**

Question:

I am working on a project using Docker, Conda, and PyTorch. The environment works perfectly on my local macOS, but I encounter the following error when running the Docker container on an Ubuntu-based image:

ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /opt/conda/envs/etl/lib/python3.8/site-packages/pyproj/../../../libproj.so.25)

Dockerfile:

FROM condaforge/mambaforge:22.11.1-4ARG PIP_EXTRA_INDEX_URLWORKDIR /appENV PYTHONUNBUFFERED 1ENV DEBIAN_FRONTEND=noninteractiveRUN apt-get update && apt-get install --no-install-recommends -y firefox-geckodriver \&& rm -rf /var/lib/apt/lists/*# Copy environment.ymlCOPY environment.yml .# Set pip index URL for private repoENV PIP_EXTRA_INDEX_URL=${PIP_EXTRA_INDEX_URL}ENV PYTHONHASHSEED 0 RUN --mount=type=cache,target=/opt/conda/pkgs conda config --set always_yes yes && \    mamba env create --file environment.yml && \    conda clean -afyCOPY . .

environment.yml:

name: etlchannels:  - conda-forge  - pytorchdependencies:  - python=3.8  - awswrangler=3.2.1  - psycopg2=2.9.3  - beautifulsoup4=4.11.1  - joblib=1.1.1  - botocore=1.34.51  - boto3=1.34.51  - selenium=4.1.0  - tqdm=4.64.1  - sqlalchemy=1.4.39  - geoalchemy2=0.13.1  - geopandas=0.12.2  - rtree=1.0.1  - scrapy=2.8.0  - pandas=1.5.2  - pyarrow=11.0.0  - openpyxl=3.0.10  - fiona=1.8.22  - pyogrio=0.5.0  - black=23.1.0  - requests=2.31.0  - dateparser=1.1.8  - pip  - pytorch  - torchvision  - torchaudio  - cpuonly  - gcc  - libstdcxx-ng>=12.2.0  # Fix for GLIBCXX version issues  - zlib>=1.2.11

as well it imports a library that has the following requirement.txt

Unidecode==1.3.8asyncpg==0.29.0boto3==1.34.132botocore==1.34.132gspread==6.1.2joblib==1.4.2packaging==24.1pandas>=2.0.0,<2.1.0psutil==6.0.0pyarrow==16.1.0python-dateutil==2.9.0.post0pytz==2024.1s3transfer==0.10.2scikit-learn==1.3.2scipy>=1.7.0,<1.12.0six==1.16.0sqlalchemy==2.0.31threadpoolctl==3.5.0tqdm==4.66.4transformers==4.41.2tzdata==2024.1

Error Description:

The issue seems to stem from the GLIBCXX version:

ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found

I’ve added libstdcxx-ng>=12.2.0 to the Conda environment file to ensure compatibility with the required version, but I still encounter the error when running the Docker container. On my local machine (macOS), the environment works without issues, but it fails in the Ubuntu-based Docker image.

Debug Attempts:

• I’ve confirmed that installing libstdcxx-ng should provide the correct GLIBCXX version, but it seems this isn’t working within the Docker image.
• Running the environment setup directly on Ubuntu (without Docker) seems to work fine. The issue is specific to the Docker container.
• I’ve tried different versions of gcc and libstdcxx-ng without success.

Question:

How can I resolve this GLIBCXX_3.4.29 error in my Docker environment? Is there a better way to manage these dependencies within Conda and Docker?

Things I have considered:

1. Manually installing the required libstdc++ version in the Docker image.
2. Using a different base image that may already have the correct GLIBCXX version.
3. Ensuring compatibility between system libraries and Conda dependencies.

Any guidance would be greatly appreciated!

Tags:

docker, conda, pytorch, ubuntu, libstdc++, python-3.8

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