ImportError in new repo

RenkuLab
1

Dear renkuers,

From a new repo (with old code), starting a renkulab session leads to the following error:

ImportError: /opt/conda/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /opt/conda/lib/python3.9/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-39-x86_64-linux-gnu.so)

From the corresponding conda environment on my laptop, code execution works fine.

According to Stackoverflow, this problem might be solved by updating the LD_LIBRARY_PATH which I don’t know how to do on renku (and whether it’s actually the problem).
[python - Anaconda ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found - Stack Overflow]

Any help is much appreciated!

Best,
Lili

2

@LiliGasser can you post the project’s Dockerfile here?

3

Something weird has happened. After more than 30 minutes of the streamlit app being open, the message disappears and the app loads. When rerunning the app, the error message is back.

Here is the Dockerfile, taken from the current streamlit renku template.

# For finding latest versions of the base image see
# https://github.com/SwissDataScienceCenter/renkulab-docker
ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.9-0.11.1
FROM ${RENKU_BASE_IMAGE}

# Uncomment and adapt if code is to be included in the image
# COPY src /code/src

# Uncomment and adapt if your R or python packages require extra linux (ubuntu) software
# e.g. the following installs apt-utils and vim; each pkg on its own line, all lines
# except for the last end with backslash '\' to continue the RUN line
#
# USER root
# RUN apt-get update && \
#    apt-get install -y --no-install-recommends \
#    apt-utils \
#    vim
# USER ${NB_USER}

# install the python dependencies
COPY requirements.txt environment.yml /tmp/
RUN conda env update -q -f /tmp/environment.yml && \
    /opt/conda/bin/pip install -r /tmp/requirements.txt && \
    conda clean -y --all && \
    conda env export -n "root"

# RENKU_VERSION determines the version of the renku CLI
# that will be used in this image. To find the latest version,
# visit https://pypi.org/project/renku/#history.
ARG RENKU_VERSION=1.4.0

# to run streamlit
COPY jupyter_notebook_config.py ~/.jupyter/

########################################################
# Do not edit this section and do not add anything below

RUN if [ -n "$RENKU_VERSION" ] ; then \
        source .renku/venv/bin/activate ; \
        currentversion=$(renku --version) ; \
        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
            pip uninstall renku -y ; \
            pip install --force renku==${RENKU_VERSION} ;\
        fi \
    fi

########################################################
4

@tolevski following your suggestion, a helloworld example works both in this repo and also in a separate minimal repo.

I found this (linux - 'GLIBCXX_3.4.30' not found for librosa in conda virtual environment (after trying out a lot of solutions)? - Stack Overflow) and wanted to check the installed scipy and gcc versions but it is not possible to open a terminal in jupyter lab. There is a Launcher Error: XSRF cookie does not match POST argument

Thanks for your support!

5

pinning to a lower scipy version in environment.yml solved the issue.