58 lines
2.6 KiB
Docker
58 lines
2.6 KiB
Docker
# Copyright 2024 DeepMind Technologies Limited
|
|
#
|
|
# AlphaFold 3 source code is licensed under CC BY-NC-SA 4.0. To view a copy of
|
|
# this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/
|
|
#
|
|
# To request access to the AlphaFold 3 model parameters, follow the process set
|
|
# out at https://github.com/google-deepmind/alphafold3. You may only use these
|
|
# if received directly from Google. Use is subject to terms of use available at
|
|
# https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
|
|
|
|
FROM nvidia/cuda:12.6.0-base-ubuntu22.04
|
|
|
|
# Some RUN statements are combined together to make Docker build run faster.
|
|
# Get latest package listing, install software-properties-common, git and wget.
|
|
# git is required for pyproject.toml toolchain's use of CMakeLists.txt.
|
|
RUN apt update --quiet \
|
|
&& apt install --yes --quiet software-properties-common \
|
|
&& apt install --yes --quiet git wget
|
|
|
|
# Get apt repository of specific Python versions. Then install Python. Tell APT
|
|
# this isn't an interactive TTY to avoid timezone prompt when installing.
|
|
RUN add-apt-repository ppa:deadsnakes/ppa \
|
|
&& DEBIAN_FRONTEND=noninteractive apt install --yes --quiet python3.11 python3-pip python3.11-venv python3.11-dev
|
|
RUN python3.11 -m venv /alphafold3_venv
|
|
ENV PATH="/hmmer/bin:/alphafold3_venv/bin:$PATH"
|
|
|
|
# Install HMMER. Do so before copying the source code, so that docker can cache
|
|
# the image layer containing HMMER.
|
|
RUN mkdir /hmmer_build /hmmer ; \
|
|
wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz --directory-prefix /hmmer_build ; \
|
|
(cd /hmmer_build && tar zxf hmmer-3.4.tar.gz && rm hmmer-3.4.tar.gz) ; \
|
|
(cd /hmmer_build/hmmer-3.4 && ./configure --prefix /hmmer) ; \
|
|
(cd /hmmer_build/hmmer-3.4 && make -j8) ; \
|
|
(cd /hmmer_build/hmmer-3.4 && make install) ; \
|
|
(cd /hmmer_build/hmmer-3.4/easel && make install) ; \
|
|
rm -R /hmmer_build
|
|
|
|
# Copy the AlphaFold 3 source code from the local machine to the container and
|
|
# set the working directory to there.
|
|
COPY . /app/alphafold
|
|
WORKDIR /app/alphafold
|
|
|
|
# Install the Python dependencies AlphaFold 3 needs.
|
|
RUN pip3 install -r dev-requirements.txt
|
|
RUN pip3 install --no-deps .
|
|
# Build chemical components database (this binary was installed by pip).
|
|
RUN build_data
|
|
|
|
# To work around a known XLA issue causing the compilation time to greatly
|
|
# increase, the following environment variable setting XLA flags must be enabled
|
|
# when running AlphaFold 3:
|
|
ENV XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
|
|
# Memory settings used for folding up to 5,120 tokens on A100 80 GB.
|
|
ENV XLA_PYTHON_CLIENT_PREALLOCATE=true
|
|
ENV XLA_CLIENT_MEM_FRACTION=0.95
|
|
|
|
CMD ["python3", "run_alphafold.py"]
|