switich to apptainer and miniforge - package versions

[christophista]

• Python version: 3.9
• Operating System: Debian

Description

Trying to install docker file in an apptainer and also switch to miniforge

What I Did

Using apptainer (1.2.5 on Debian bookworm) I tried to underneath definition file to port NeuralPLexer to apptainer. Furthermore, I exchanged anaconda for miniforge to circumvent licensing issues. However, there seems to be a problem with numpy, pandas or mendeleev packages.

Thus, would anybody who has a working docker environment please share their conda environment with the exact package versions? I somehow suspect that newer version might cause this problem.

Thank you in advance

Bootstrap: docker
From: nvidia/cuda:11.7.1-devel-ubuntu22.04
Stage: spython-base


%arguments
  

%files

%post

  ## ###################################################################################################################
  echo -e "0. non-package related sw."
  apt-get update \
    && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
        make \
        git \
        wget \
        tzdata \
        awscli \
        tree \
        nano \
    && rm -rf /var/lib/apt/lists/* \
    && apt-get autoremove -y \
    && apt-get clean



  ## ###################################################################################################################
  echo -e "1. Installing Miniforge"
  wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
  bash Miniforge3-$(uname)-$(uname -m).sh -b
  PATH=/root/miniforge3/bin/:$PATH
  . "/root/miniforge3/etc/profile.d/conda.sh"
  cat /root/.bashrc
  conda activate /root/miniforge3


  
  ## ###################################################################################################################
  conda create -n NeuralPLexer python=3.9
  echo "conda activate NeuralPLexer" >> ~/.bashrc

  conda run -n NeuralPLexer pip install \
    pandas==2.0.0

  conda run -n NeuralPLexer pip install \
    torch==1.13.1+cu117 \
    torchvision==0.14.1+cu117 \
    torchaudio==0.13.1 \
    --extra-index-url https://download.pytorch.org/whl/cu117 --no-cache-dir

  conda run -n NeuralPLexer pip install \
    torch-scatter==2.1.0 \
    -f https://data.pyg.org/whl/torch-1.13.1+cu117.html --no-cache-dir

  conda run -n NeuralPLexer pip install \
    "git+https://github.com/facebookresearch/pytorch3d.git" \
    --force-reinstall --no-deps --no-cache-dir



  ## ###################################################################################################################
  git clone https://github.com/aqlaboratory/openfold.git
  cd openfold && \
    sed -i 's/std=c++14/std=c++17/g' setup.py && \
    conda run -n NeuralPLexer pip install . && \
    cd ../ && \
    rm -rf openfold


  
  ## ###################################################################################################################
  git clone https://github.com/zrqiao/NeuralPLexer.git && \
    cd NeuralPLexer && \
    conda run -n NeuralPLexer conda env update --file NeuralPLexer.yml && \
    conda run -n NeuralPLexer conda clean -afy && \
    conda run -n NeuralPLexer make install

  

  echo -e "\n\ncleanup\n"
  echo -e "\n\nall done...\n"


%environment


%runscript 
  echo "user command"
  echo "provided: '$@'"
  echo ""
  echo #######################################################################################################
  
  . "/root/miniforge3/etc/profile.d/conda.sh"
  conda activate NeuralPLexer
  exec $@


%startscript
  echo "start not supported"
  exit