Olamide Isreal
f971fd0e21
- Nextflow pipeline using chai1 Docker image from Harbor - S3-based input/output paths (s3://omic/eureka/chai-lab/) - GPU-accelerated protein folding with MSA support Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
83 lines
2.8 KiB
Docker
Executable File
83 lines
2.8 KiB
Docker
Executable File
FROM ubuntu:22.04 AS chailab-baseimage
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ENV \
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LANG=C.UTF-8 \
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LC_ALL=C.UTF-8 \
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# config for apt
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DEBIAN_FRONTEND=noninteractive \
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# default editor for git cli
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EDITOR=vim \
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# keep (large) mypy cache outside of working tree
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MYPY_CACHE_DIR='/tmp/.chai_lab_mypy_cache' \
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# always flush output from python
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PYTHONUNBUFFERED=TRUE \
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# enable fault handler (print tracebacks even after segfault or NCCL errors).
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PYTHONFAULTHANDLER=1 \
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# keep __pycache__ out of working tree
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PYTHONPYCACHEPREFIX='/tmp/.chai_lab_pycache'
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RUN --mount=type=cache,target=/var/cache/apt \
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apt-get -qq update \
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&& apt-get -qq install -y \
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# common things
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gnupg ca-certificates wget git curl aria2 lsb-release tzdata \
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rsync sudo tree htop tmux unzip \
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clang \
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# for direct ssh into container
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openssh-server socat \
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# provides `fuser` command
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psmisc \
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# RDMA/InfiniBand
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libibverbs1 librdmacm1 \
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# text editors, needed by git cli
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nano vim \
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build-essential libstdc++6 \
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# python
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python3.10 python3.10-dev \
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# (run continues)
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# stop git from complaining about dubious ownership.
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&& git config --global --add safe.directory "*" \
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#
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# cuda softlinking is needed in podman, but not docker
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&& ln -s /lib/x86_64-linux-gnu/libcuda.so.1 /lib/x86_64-linux-gnu/libcuda.so \
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&& ldconfig /lib/x86_64-linux-gnu/ \
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# setup timezone, to $TZ, ubuntu-specific
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# && ln -fs /usr/share/zoneinfo/$TZ /etc/localtime \
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&& dpkg-reconfigure --frontend noninteractive tzdata \
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# change default shell to bash (has no effect during building)
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&& chsh -s /bin/bash
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ENV \
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# expose CUDA libraries. Now that we don't build anything this is likely redundant
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LD_LIBRARY_PATH="/usr/local/cuda/lib64/stubs/:${LD_LIBRARY_PATH:-}" \
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# Set uv timeout to larger value to account for slow download time of nvidia-cudnn-cu12
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UV_HTTP_TIMEOUT=1000 \
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# where virtual env will be installed
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VIRTUAL_ENV=/opt/venv
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# Install dependencies in virtualenv
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COPY ./requirements.in /tmp/requirements.in
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# from https://pythonspeed.com/articles/activate-virtualenv-dockerfile/
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# a trick to have virtualenv "always activated"
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ENV PATH="$VIRTUAL_ENV/bin:$PATH"
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RUN --mount=type=cache,target=/root/.cache/uv \
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# Install uv
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curl -LsSf https://astral.sh/uv/0.5.4/install.sh | sh \
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&& . $HOME/.local/bin/env \
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&& uv venv --no-python-downloads $VIRTUAL_ENV \
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# this is sh, not bash, so . not source
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&& . $VIRTUAL_ENV/bin/activate \
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&& uv pip install uv pip -r /tmp/requirements.in
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# making sure envvars are set in all shells
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RUN echo "PATH=\"$PATH\"" >> /etc/environment \
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&& echo "LANG=\"$LANG\"" >> /etc/environment \
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&& echo "LC_ALL=\"$LC_ALL\"" >> /etc/environment \
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&& echo "LD_LIBRARY_PATH=\"$LD_LIBRARY_PATH\"" >> /etc/environment \
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&& echo "EDITOR=\"$EDITOR\"" >> /etc/environment
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# no startup command. |