python: can't open file '/app/alphafold/run_alphafold.py': [Errno 13] Permission denied (related to Ubuntu update?)

[sz-1002]

Hi!

I encountered a new error running AlphaFold multimer 2.3.0 after re-building the Docker image (re-building because I was trying to see if changing versions of CUDA or jax could at least temporarily fix the CUDA_ERROR_ILLEGAL_ADDRESS error #667):

python: can't open file '/app/alphafold/run_alphafold.py': [Errno 13] Permission denied)

To me this looks like something wrong with the Docker image, but docker build -f docker/Dockerfile -t alphafold . gives no error (see below) (this is using the default Dockerfile).

The same commands worked fine before, and the only difference I can think of is I just updated the packages in Ubuntu (sudo apt update & upgrade). Do you think this is an issue with the package updates, or some other problem? OS is Ubuntu 20.04 LTS.

Thank you very much for your help!!

---

Output of docker build -f docker/Dockerfile -t alphafold .:

Sending build context to Docker daemon  34.93MB
Step 1/18 : ARG CUDA=11.1.1
Step 2/18 : FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu18.04
 ---> cd358584cc21
Step 3/18 : ARG CUDA
 ---> Using cache
 ---> accb97b87cea
Step 4/18 : SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 ---> Using cache
 ---> 17f0f9efe7e5
Step 5/18 : RUN apt-get update     && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y         build-essential         cmake         cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-})         git         hmmer         kalign         tzdata         wget     && rm -rf /var/lib/apt/lists/*     && apt-get autoremove -y     && apt-get clean
 ---> Using cache
 ---> 0864b73d6980
Step 6/18 : RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite     && mkdir /tmp/hh-suite/build     && pushd /tmp/hh-suite/build     && cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite ..     && make -j 4 && make install     && ln -s /opt/hhsuite/bin/* /usr/bin     && popd     && rm -rf /tmp/hh-suite
 ---> Using cache
 ---> dc08894bbed5
Step 7/18 : RUN wget -q -P /tmp   https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh     && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda     && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
 ---> Using cache
 ---> 8d934078b34c
Step 8/18 : ENV PATH="/opt/conda/bin:$PATH"
 ---> Using cache
 ---> 78dda2de761b
Step 9/18 : RUN conda install -qy conda==4.13.0     && conda install -y -c conda-forge       openmm=7.5.1       cudatoolkit==${CUDA_VERSION}       pdbfixer       pip       python=3.8       && conda clean --all --force-pkgs-dirs --yes
 ---> Using cache
 ---> b386b78a8e38
Step 10/18 : COPY . /app/alphafold
 ---> Using cache
 ---> 51240e950dc8
Step 11/18 : RUN wget -q -P /app/alphafold/alphafold/common/   https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
 ---> Using cache
 ---> 6a7fea94a5d6
Step 12/18 : RUN pip3 install --upgrade pip --no-cache-dir     && pip3 install -r /app/alphafold/requirements.txt --no-cache-dir     && pip3 install --upgrade --no-cache-dir       jax==0.3.25       jaxlib==0.3.25+cuda11.cudnn805       -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 ---> Using cache
 ---> a8d0e25f2fb8
Step 13/18 : WORKDIR /opt/conda/lib/python3.8/site-packages
 ---> Using cache
 ---> 0481fbf8e8ac
Step 14/18 : RUN patch -p0 < /app/alphafold/docker/openmm.patch
 ---> Using cache
 ---> a62a20fed700
Step 15/18 : RUN chmod u+s /sbin/ldconfig.real
 ---> Using cache
 ---> 1ec560583846
Step 16/18 : WORKDIR /app/alphafold
 ---> Using cache
 ---> 3eb0ad557f20
Step 17/18 : RUN echo $'#!/bin/bash\nldconfig\npython /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh   && chmod +x /app/run_alphafold.sh
 ---> Using cache
 ---> 2575cdda7311
Step 18/18 : ENTRYPOINT ["/app/run_alphafold.sh"]
 ---> Using cache
 ---> 3c6b60454cad
Successfully built 3c6b60454cad
Successfully tagged alphafold:latest

(There were warnings about running pip as root, e.g. WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv)

[alexanderimanicowenrivers]

Does fixing permissions on the code help? sudo chmod 755 --recursive alphafold.

[sz-1002]

@alexanderimanicowenrivers

Nope, still the same error.
But, downloading a fresh copy of AlphaFold2 (v2.3.1) fixed this problem somehow.

Thanks a lot!