Question: Execution error (stopped and won't proceed)

I attempted to launch localcolabfold from the following Docker image, but it stopped partway through execution and wouldn't proceed.

FROM nvidia/cuda:11.8.0-cudnn8-devel-ubuntu20.04

ENV PATH="/root/miniconda3/bin:${PATH}"
ARG PATH="/root/miniconda3/bin:${PATH}"
WORKDIR /root

RUN ln -sf /usr/share/zoneinfo/Asia/Tokyo /etc/localtime

RUN apt-get update && apt-get install -y --no-install-recommends \
    build-essential \
    cmake \
    curl \
    dssp \
    git \
    vim \
    wget \     
    ca-certificates \
    libjpeg-dev \
    libpng-dev && \
    rm -rf /var/lib/apt/lists/* \
    && wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && mkdir /root/.conda \
    && bash Miniconda3-latest-Linux-x86_64.sh -b \
    && rm -f Miniconda3-latest-Linux-x86_64.sh \
    && conda --version

RUN conda update -n base -c defaults conda \
    && conda config --set ssl_verify no \
    && conda init bash \
    && conda clean -afy

ARG env_name=localcolabfold
RUN conda create -n ${env_name} -y \
    python=3.8 \
    pytorch=1.11 \
    pyg \
    jupyterlab \
    biopython \
    abnumber \
    anarci \
    logomaker \
    numpy==1.21.5 \
    pandas \
    pathlib2 \
    matplotlib \
    seaborn \
    scipy==1.7.3 \
    requests==2.28.1 \
    packaging pip \
    openmm==7.7.0 \
    pdbfixer \
    -c pytorch -c dglteam -c pyg -c conda-forge -c bioconda

# Acitivate environment
ENV CONDA_DEFAULT_ENV ${env_name}

# Switch default environment
RUN echo "conda activate ${env_name}" >> ~/.bashrc
ENV PATH /opt/conda/envs/${env_name} /bin:$PATH

WORKDIR /work
RUN wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/install_colabbatch_linux.sh
RUN bash install_colabbatch_linux.sh
RUN cd localcolabfold

ENV PATH="/work/localcolabfold/colabfold-conda/bin:${PATH}"

/work/localcolabfold/colabfold-conda/bin/colabfold_batch --amber --num-recycle 3 --use-gpu-relax inputfile outputdir

2024-04-02 15:00:28,123 Running colabfold 1.5.5 (61df3b853140ca79dbdf64349824beb14364ebfd)

WARNING: You are welcome to use the default MSA server, however keep in mind that it's a
limited shared resource only capable of processing a few thousand MSAs per day. Please
submit jobs only from a single IP address. We reserve the right to limit access to the
server case-by-case when usage exceeds fair use. If you require more MSAs: You can
precompute all MSAs with `colabfold_search` or host your own API and pass it to `--host-url`

2024-04-02 15:00:28,789 Running on GPU
2024-04-02 15:00:29,077 generated new fontManager
2024-04-02 15:00:29,336 Found 6 citations for tools or databases
2024-04-02 15:00:29,336 Query 1/1: sp_P61823 (length 150)
2024-04-02 15:00:29,672 Setting max_seq=512, max_extra_seq=2404

Regarding the setup, initially, the GPU was not recognized (no GPU detected, will be using CPU). And after installing cuDNN, I encountered the aforementioned issue.

If anyone knows a solution, I would appreciate your guidance.

YoshitakaMo / localcolabfold

Question: Execution error (stopped and won't proceed) #225