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Build docker images to compile mmseqs and foldseek
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‎.github/workflows/docker.yml‎

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name: Create and publish Docker images
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on:
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push:
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branches:
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- "main"
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release:
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types: [published]
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workflow_dispatch:
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inputs:
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tag:
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required: true
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type: string
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description: "Docker tag"
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latest:
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default: false
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type: boolean
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description: "Mark as latest"
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: ${{ github.repository }}
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jobs:
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build-and-push-gpu-builder:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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strategy:
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fail-fast: false
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matrix:
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include:
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- suffix: x86_64
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dockerfile: Dockerfile.GPU-manylinux2014
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- suffix: sbsa
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dockerfile: Dockerfile.GPU-buster-cross-sbsa
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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- name: Log in to the Container registry
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uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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flavor: |
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suffix=-${{ matrix.suffix }},onlatest=true
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- name: Tag for workflow_dispatch
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id: dispatch_tag
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run: |
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if [ -n "$TAG" ]; then
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echo "tag=$FULL_TAG" >> $GITHUB_OUTPUT
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fi
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if [ "$LATEST" = "true" ]; then
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echo "latest=$LATEST_TAG" >> $GITHUB_OUTPUT
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fi
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env:
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FULL_TAG: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.event.inputs.tag }}
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LATEST_TAG: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest
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TAG: ${{ github.event.inputs.tag }}
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LATEST: ${{ github.event.inputs.latest }}
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- name: Build and push Docker image
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uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
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with:
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context: .
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file: ${{ matrix.dockerfile }}
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platforms: linux/amd64
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push: true
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build-args: |
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GPU=1
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tags: |
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${{ steps.meta.outputs.tags }}
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${{ steps.dispatch_tag.outputs.tag }}
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${{ steps.dispatch_tag.outputs.latest }}
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labels: ${{ steps.meta.outputs.labels }}

‎Dockerfile.GPU-buster-cross-sbsa‎

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FROM debian:buster
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ARG VER="12-6"
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RUN dpkg --add-architecture arm64
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RUN sed -i s/deb.debian.org/archive.debian.org/g /etc/apt/sources.list; \
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sed -i s/security.debian.org/archive.debian.org/g /etc/apt/sources.list; \
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apt-get update; \
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apt-get -y install -o APT::Immediate-Configure=false \
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git curl wget vim ninja-build crossbuild-essential-arm64 zlib1g-dev:arm64 libbz2-dev:arm64 software-properties-common
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RUN wget https://github.com/Kitware/CMake/releases/download/v3.31.0/cmake-3.31.0-linux-x86_64.sh; \
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chmod +x cmake-3.31.0-linux-x86_64.sh; \
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./cmake-3.31.0-linux-x86_64.sh --skip-license --prefix=/usr/local;
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RUN wget -O cuda-x64.deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb
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RUN wget -O cuda-sbsa.deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/cross-linux-sbsa/cuda-keyring_1.1-1_all.deb
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RUN dpkg -i cuda-x64.deb && dpkg -i cuda-sbsa.deb
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RUN apt-get update
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RUN apt-get install -y cuda-nvcc-${VER} cuda-nvcc-cross-sbsa-${VER} cuda-cudart-cross-sbsa-${VER} libcublas-cross-sbsa-${VER}
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RUN curl https://sh.rustup.rs -sSf | \
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sh -s -- --default-toolchain stable -y
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ENV PATH=/root/.cargo/bin:$PATH

‎Dockerfile.GPU-manylinux2014‎

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FROM quay.io/pypa/manylinux2014_x86_64
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ARG VER="12-6"
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ARG ARCH="x86_64"
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# CUDA
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RUN yum install -y yum-utils
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RUN yum-config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
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RUN yum -y install cuda-nvcc-${VER}.${ARCH} cuda-cudart-devel-${VER}.${ARCH} libcublas-devel-${VER}.${ARCH}
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RUN echo "/usr/local/cuda/lib64" >> /etc/ld.so.conf.d/999_nvidia_cuda.conf
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ENV PATH="/usr/local/cuda/bin:${PATH}"
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ENV LD_LIBRARY_PATH="/usr/local/cuda/lib64:${LD_LIBRARY_PATH}"
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ENV CUDA_HOME=/usr/local/cuda
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ENV CUDA_ROOT=/usr/local/cuda
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ENV CUDA_PATH=/usr/local/cuda
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ENV CUDADIR=/usr/local/cuda
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# Build system
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RUN yum install -y git curl wget vim zlib-devel bzip2-devel ninja-build centos-release-scl
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RUN mv /etc/yum.repos.d/CentOS-SCLo-scl.repo /etc/yum.repos.d/CentOS-SCLo-scl.repo.disabled
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RUN yum install -y devtoolset-11-gcc devtoolset-11-gcc-c++ devtoolset-11-libatomic-devel
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ENV CC=/opt/rh/devtoolset-11/root/bin/gcc
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ENV CXX=/opt/rh/devtoolset-11/root/bin/g++
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ENV CUDAHOSTCXX=/opt/rh/devtoolset-11/root/bin/g++
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ENV CUDACXX=/usr/local/cuda/bin/nvcc
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ENV LIBGCC=/opt/rh/devtoolset-11/root/usr/lib/gcc/x86_64-redhat-linux/11
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# cmake
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RUN wget https://github.com/Kitware/CMake/releases/download/v3.31.0/cmake-3.31.0-linux-x86_64.sh; \
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chmod +x cmake-3.31.0-linux-x86_64.sh; \
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./cmake-3.31.0-linux-x86_64.sh --skip-license --prefix=/usr/local;
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RUN mkdir /deps; \
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cd /deps; \
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wget https://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz; \
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tar xzvf bzip2-1.0.8.tar.gz; \
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cd bzip2-1.0.8; \
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make install PREFIX=/deps;
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RUN cd /deps; \
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wget https://www.zlib.net/zlib-1.3.1.tar.gz; \
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tar xzvf zlib-1.3.1.tar.gz; \
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cd zlib-1.3.1; \
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./configure --prefix=/deps --static; \
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make install;
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# install toolchain
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RUN curl https://sh.rustup.rs -sSf | \
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sh -s -- --default-toolchain stable -y
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ENV PATH=/root/.cargo/bin:$PATH
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