update
This commit is contained in:
lingyu zeng
192
Dockerfile.gromacs_amber
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192
Dockerfile.gromacs_amber
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# syntax=docker/dockerfile:1
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# NOTE: Building this image require's docker version >= 23.0.
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#
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# For reference:
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# - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
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ARG TAG_VERSION="12.4.1"
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FROM nvidia/cuda:${TAG_VERSION}-cudnn-devel-ubuntu22.04
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ARG HTTP_PROXY
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ARG HTTPS_PROXY
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ENV http_proxy=${HTTP_PROXY}
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ENV https_proxy=${HTTPS_PROXY}
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
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ARG ROOT_PASSWD="root"
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ENV ROOT_PASSWD=${ROOT_PASSWD}
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ENV SSH_PORT=2222
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WORKDIR /root
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SHELL ["/bin/bash", "-c"]
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# base tools
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RUN <<EOT
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#!/bin/bash
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apt-get update
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apt-get install -y libgl1-mesa-glx bash-completion wget curl htop jq vim bash libaio-dev build-essential openssh-server openssh-client python3 python3-pip python3-venv bzip2
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apt-get install -y --no-install-recommends software-properties-common build-essential autotools-dev nfs-common pdsh cmake g++ gcc curl wget vim tmux emacs less unzip htop iftop iotop ca-certificates openssh-client openssh-server rsync iputils-ping net-tools sudo llvm-dev re2c
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add-apt-repository ppa:git-core/ppa -y
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apt-get install -y git libnuma-dev wget
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pip install pipx
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pipx install nvitop
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pipx ensurepath
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. ~/.bashrc
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# Configure SSH for password and public key authentication
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mkdir ~/.ssh
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# 创建或覆盖 SSH 配置文件 ~/.ssh/config
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# - Host *: 针对所有主机的通用配置
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# - ForwardAgent yes: 启用 SSH 代理转发，允许通过本地的 SSH 代理进行身份验证
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# - StrictHostKeyChecking no: 禁用主机密钥检查，自动接受新的主机密钥（适用于自动化环境）
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printf "Host * \n ForwardAgent yes\nHost *\n StrictHostKeyChecking no" > ~/.ssh/config
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cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
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sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
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sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
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sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
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sed -i 's/^\(\s*\)GSSAPIAuthentication yes/\1GSSAPIAuthentication no/' /etc/ssh/ssh_config
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sed -i "s/^#Port 22/Port ${SSH_PORT}/" /etc/ssh/sshd_config
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sudo sed -i "s/# Port 22/Port ${SSH_PORT}/" /etc/ssh/ssh_config
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ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
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cat ~/.ssh/id_rsa.pub >> ~/.ssh/auth
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cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys
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cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys2
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chmod 600 /root/.ssh/authorized_keys
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chmod 600 /root/.ssh/authorized_keys2
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mkdir /var/run/sshd
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echo "root:${ROOT_PASSWD}" | chpasswd
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mkdir -p ~/.pip
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# install pixi
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curl -fsSL https://pixi.sh/install.sh | bash
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EOT
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ARG FFTW_VERSION="3.3.10"
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ENV FFTW_VERSION=${FFTW_VERSION}
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ENV PATH=/usr/local/fftw:$PATH
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# 安装fftw
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RUN <<EOT
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#!/bin/bash
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wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
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tar zxvf fftw-${FFTW_VERSION}.tar.gz
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cd fftw-${FFTW_VERSION}
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./configure --prefix=/usr/local/fftw --enable-sse2 --enable-avx --enable-float --enable-avx2 --enable-shared # 若CPU支持AVX512指令集，且有多于1个AVX512 FMA单元，则可加上--enable-avx512以进一步提升性能
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make -j$(nproc)
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make install
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EOT
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# 安装openmpi
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ENV MPI_HOME=/usr/local/openmpi
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ENV PATH=${MPI_HOME}/bin:/usr/bin:$PATH
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ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64:${MPI_HOME}/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
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ENV LIBRARY_PATH=/usr/local/cuda/lib64:${LIBRARY_PATH}
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ENV CPATH=/usr/local/cuda/include:${MPI_HOME}/include:${CUDA_HOME}/include:$CPATH
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# export C_INCLUDE_PATH=/usr/local/cuda/include:$C_INCLUDE_PATH
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# export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
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# export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
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RUN <<EOT
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#!/bin/bash
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apt update && apt install -y autoconf automake libtool flex
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/usr/bin/python3 -m pip install cython
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git clone --recursive https://github.com/open-mpi/ompi.git
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cd ompi
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git checkout main
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# make clean
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# make distclean
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./autogen.pl
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mkdir build
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cd build
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../configure --with-cuda=/usr/local/cuda --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-python=/usr/bin/python3
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make -j$(nproc)
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make install
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# 验证CUDA支持
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cat <<EOF > ./test_mpi_cuda.cu
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#include <mpi.h>
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#include <cuda_runtime.h>
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#include <stdio.h>
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__global__ void hello_cuda() {
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printf("Hello from CUDA kernel! Thread id: %d\n", threadIdx.x);
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}
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int main(int argc, char **argv) {
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MPI_Init(&argc, &argv);
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int rank;
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MPI_Comm_rank(MPI_COMM_WORLD, &rank);
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printf("Hello from MPI process %d!\n", rank);
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// Launch CUDA kernel
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hello_cuda<<<1, 10>>>();
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cudaDeviceSynchronize(); // Wait for the CUDA kernel to finish
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MPI_Finalize();
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return 0;
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}
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EOF
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nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/include -L${MPI_HOME}/lib -lcudart -lmpi
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# mpirun --allow-run-as-root -np 2 ./test_mpi_cuda
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EOT
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# 安装plumed
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ARG PLUMED_VERSION="2.9.1"
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ENV PLUMED_VERSION=${PLUMED_VERSION}
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ENV LD_LIBRARY_PATH=/usr/local/plumed/lib:$LD_LIBRARY_PATH
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ENV PATH=/usr/local/plumed:/usr/local/plumed/bin:$PATH
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RUN <<EOT
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#!/bin/bash
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# git clone https://github.com/plumed/plumed2
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# cd plumed2
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# git checkout v${PLUMED_VERSION}
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curl -L -o plumed-${PLUMED_VERSION}.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_VERSION}/plumed-${PLUMED_VERSION}.tgz
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tar zxvf plumed-${PLUMED_VERSION}.tar.gz
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cd plumed-${PLUMED_VERSION}
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./configure --prefix=/usr/local/plumed
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make -j$(nproc)
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make install
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EOT
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# 安装gromacs
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ARG GROMACS_VERSION="2022.5"
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ENV GROMACS_VERSION=${GROMACS_VERSION}
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ENV GROMACS_HOME=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
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ENV PATH=PATH=$GROMACS_HOME/bin:$PATH
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RUN <<EOT
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#!/bin/bash
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wget -c https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz
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tar zxvf gromacs-${GROMACS_VERSION}.tar.gz
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cd gromacs-${GROMACS_VERSION}
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### patch the plumed
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# plumed-patch -p
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plumed-patch -p -e gromacs-${GROMACS_VERSION}
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mkdir build
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cd build
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cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} \
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-DGMX_BUILD_OWN_FFTW=ON \
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-DREGRESSIONTEST_DOWNLOAD=ON \
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-DGMX_GPU=CUDA \
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-DGMX_MPI=ON
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make -j$(nproc)
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make install
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echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
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EOT
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COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
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ENV DOWNLOAD_MINICONDA="False"
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# install ambertools
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RUN <<EOT
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#!/bin/bash
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python3 -m pip install https://blog.csdn.net/GHZ2443063059/article/details/141103550
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# 解压 Amber24
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tar -xjf Amber24.tar.bz2
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# 解压 AmberTools24
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tar -xjf AmberTools24.tar.bz2
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# 清理解压后的 .tar.bz2 文件（可选）
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rm Amber24.tar.bz2 AmberTools24.tar.bz2
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EOT
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RUN <<EOT
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#!/bin/bash
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apt-get clean && rm -rf /var/lib/apt/lists/*
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EOT
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EXPOSE 2222
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CMD ["/usr/sbin/sshd", "-D"]
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