temp save
This commit is contained in:
@@ -22,26 +22,13 @@ ENV SSH_PORT=2222
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WORKDIR /root
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WORKDIR /root
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SHELL ["/bin/bash", "-c"]
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SHELL ["/bin/bash", "-c"]
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# Replace sources.list with Aliyun mirror
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RUN <<EOT
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#!/bin/bash
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cp /etc/apt/sources.list /etc/apt/sources.list_bak
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cat << EOF > /etc/apt/sources.list
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deb https://mirrors.aliyun.com/ubuntu/ jammy main restricted universe multiverse
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deb-src https://mirrors.aliyun.com/ubuntu/ jammy main restricted universe multiverse
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deb https://mirrors.aliyun.com/ubuntu/ jammy-security main restricted universe multiverse
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deb-src https://mirrors.aliyun.com/ubuntu/ jammy-security main restricted universe multiverse
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deb https://mirrors.aliyun.com/ubuntu/ jammy-updates main restricted universe multiverse
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deb-src https://mirrors.aliyun.com/ubuntu/ jammy-updates main restricted universe multiverse
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deb https://mirrors.aliyun.com/ubuntu/ jammy-backports main restricted universe multiverse
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deb-src https://mirrors.aliyun.com/ubuntu/ jammy-backports main restricted universe multiverse
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EOF
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EOT
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# Install base tools for compilation
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# Install base tools for compilation
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RUN <<EOT
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RUN <<EOT
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#!/bin/bash
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#!/bin/bash
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apt update && apt install -y --no-install-recommends \
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apt-get update && apt-get install -y tzdata
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ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
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echo "Asia/Shanghai" > /etc/timezone
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apt-get install -y --no-install-recommends \
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build-essential \
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build-essential \
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autotools-dev \
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autotools-dev \
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libaio-dev \
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libaio-dev \
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@@ -70,29 +57,39 @@ apt update && apt install -y --no-install-recommends \
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pkg-config \
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pkg-config \
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cmake \
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cmake \
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bzip2 \
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bzip2 \
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curl \
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bzip2 \
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tar \
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tar \
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curl \
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curl \
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wget \
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wget \
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jq
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jq \
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openssh-client \
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openssh-server \
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htop jq \
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libgl1-mesa-glx bash-completion \
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iftop iotop ca-certificates
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pip install pipx
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pip install pipx
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pipx install nvitop
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pipx install nvitop
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pipx ensurepath
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pipx ensurepath
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. ~/.bashrc
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. ~/.bashrc
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EOT
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EOT
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RUN echo "Check wget version" && wget --version
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# SSH setup
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# Install Modules for environment management
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COPY ./file/modules-5.4.0.tar.gz /root
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RUN <<EOT
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RUN <<EOT
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#!/bin/bash
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#!/bin/bash
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tar zxvf modules-5.4.0.tar.gz
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mkdir ~/.ssh
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cd modules-5.4.0
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printf "Host * \n ForwardAgent yes\nHost *\n StrictHostKeyChecking no" > ~/.ssh/config
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./configure --prefix=/opt/modules --bindir=/opt/modules/bin --libdir=/opt/modules/lib --disable-libtclenvmodules
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cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
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make -j$(nproc)
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sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
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make install
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sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
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echo "source /opt/modules/init/profile.sh" >> /etc/profile
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sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
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echo "source /opt/modules/init/profile.sh" >> ~/.bashrc
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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 ${SSH_PORT}/" /etc/ssh/sshd_config
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ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
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cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
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chmod 600 /root/.ssh/authorized_keys
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mkdir /var/run/sshd
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echo "root:${ROOT_PASSWD}" | chpasswd
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EOT
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EOT
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# Install FFTW
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# Install FFTW
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@@ -192,14 +189,6 @@ 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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echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
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EOT
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EOT
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# Install AmberTools and Amber
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COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
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RUN <<EOT
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#!/bin/bash
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tar -xjvf Amber24.tar.bz2
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tar -xjvf AmberTools24.tar.bz2
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EOT
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# Install Boost
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# Install Boost
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COPY file/boost_1_86_0.tar.gz /root
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COPY file/boost_1_86_0.tar.gz /root
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ENV MODULEPATH=/opt/modulefiles/boost:$MODULEPATH
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ENV MODULEPATH=/opt/modulefiles/boost:$MODULEPATH
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@@ -233,32 +222,6 @@ echo "source /opt/intel/setvars.sh" >> ~/.bashrc
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echo "source /opt/intel/onemkl/setvars.sh" >> ~/.bashrc
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echo "source /opt/intel/onemkl/setvars.sh" >> ~/.bashrc
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EOT
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EOT
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# SSH setup
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RUN <<EOT
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#!/bin/bash
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mkdir ~/.ssh
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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 ${SSH_PORT}/" /etc/ssh/sshd_config
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ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
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cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
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chmod 600 /root/.ssh/authorized_keys
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mkdir /var/run/sshd
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echo "root:${ROOT_PASSWD}" | chpasswd
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EOT
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# Timezone setup
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RUN <<EOT
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#!/bin/bash
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apt-get install -y tzdata
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ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
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echo "Asia/Shanghai" > /etc/timezone
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EOT
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# Install micromamba silently
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# Install micromamba silently
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WORKDIR /root
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WORKDIR /root
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ENV BIN_FOLDER=/usr/local/bin
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ENV BIN_FOLDER=/usr/local/bin
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@@ -284,6 +247,16 @@ RUN <<EOT
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git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
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git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
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EOT
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EOT
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# Install AmberTools and Amber
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COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
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RUN <<EOT
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#!/bin/bash
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tar -xjvf Amber24.tar.bz2
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tar -xjvf AmberTools24.tar.bz2
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EOT
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# install mmgbsa
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# Final cleanup
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# Final cleanup
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RUN <<EOT
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RUN <<EOT
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#!/bin/bash
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#!/bin/bash
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@@ -313,8 +286,8 @@ COPY --from=build-env /usr/local/ucx /usr/local/ucx
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COPY --from=build-env /usr/local/openmpi /usr/local/openmpi
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COPY --from=build-env /usr/local/openmpi /usr/local/openmpi
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COPY --from=build-env /usr/local/plumed /usr/local/plumed
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COPY --from=build-env /usr/local/plumed /usr/local/plumed
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COPY --from=build-env /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
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COPY --from=build-env /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
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COPY --from=build-env /opt/micromamba /opt/micromamba
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COPY --from=build-env /opt /opt
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COPY --from=build-env /usr/local/bin/micromamba /usr/local/bin/micromamba
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COPY --from=build-env /usr/local/bin /usr/local/bin
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COPY --from=build-env /root/.bashrc /root/.bashrc
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COPY --from=build-env /root/.bashrc /root/.bashrc
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# COPY --from=build-env /root/.condarc /root/.condarc # Copy micromamba config file
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# COPY --from=build-env /root/.condarc /root/.condarc # Copy micromamba config file
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# COPY --from=build-env /root/.mambarc /root/.mambarc # Copy micromamba config file (if exists)
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# COPY --from=build-env /root/.mambarc /root/.mambarc # Copy micromamba config file (if exists)
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@@ -323,12 +296,39 @@ COPY --from=build-env /opt/intel/onemkl /opt/intel/onemkl
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COPY --from=build-env /opt/boost /opt/boost
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COPY --from=build-env /opt/boost /opt/boost
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COPY --from=build-env /opt/modulefiles /opt/modulefiles
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COPY --from=build-env /opt/modulefiles /opt/modulefiles
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COPY --from=build-env /root/.ssh /root/.ssh
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COPY --from=build-env /root/.ssh /root/.ssh
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# COPY --from=build-env /etc/ssh/sshd_config /etc/ssh/sshd_config
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COPY --from=build-env /etc/ssh/sshd_config /etc/ssh/sshd_config
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COPY --from=build-env /var/run/sshd /var/run/sshd
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COPY --from=build-env /var/run/sshd /var/run/sshd
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COPY --from=build-env /root/.local /root/.local
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# Set up micromamba environment
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# Set up micromamba environment
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||||||
RUN <<EOT
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RUN <<EOT
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||||||
#!/bin/bash
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#!/bin/bash
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||||||
|
apt update && apt install -y --no-install-recommends tcl-dev \
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||||||
|
gcc \
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||||||
|
grep \
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||||||
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environment-modules \
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||||||
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tcl-devel \
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||||||
|
vim \
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||||||
|
bzip2 \
|
||||||
|
tar \
|
||||||
|
curl \
|
||||||
|
wget \
|
||||||
|
jq \
|
||||||
|
openssh-client \
|
||||||
|
openssh-server \
|
||||||
|
htop jq \
|
||||||
|
libgl1-mesa-glx bash-completion \
|
||||||
|
iftop iotop ca-certificates
|
||||||
|
mkdir -p ~/.local/modules
|
||||||
|
sudo apt install environment-modules tcl-devel
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||||||
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export HTTPS_PROXY="http://127.0.0.1:20171"
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||||||
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export HTTP_PROXY="http://127.0.0.1:20171"
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wget https://sourceforge.net/projects/modules/files/Modules/modules-5.5.0/modules-5.5.0.tar.gz/download
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||||||
|
curl -LJO https://github.com/cea-hpc/modules/releases/download/v5.5.0/modules-5.5.0.tar.gz
|
||||||
|
tar xfz modules-5.5.0.tar.gz
|
||||||
|
./configure --prefix=$HOME/.local/modules --with-tcl-lib=/usr/local/tools/tcl/lib --with-tcl-inc=/usr/local/tools/tcl/include --modulefilesdir=$HOME/.local/modules/modulefiles
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||||||
|
make
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||||||
|
make install
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||||||
# Add micromamba to PATH
|
# Add micromamba to PATH
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||||||
echo 'export PATH=/usr/local/bin:$PATH' >> /root/.bashrc
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echo 'export PATH=/usr/local/bin:$PATH' >> /root/.bashrc
|
||||||
# Initialize micromamba for bash
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# Initialize micromamba for bash
|
||||||
@@ -359,5 +359,5 @@ EOF
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|||||||
EOT
|
EOT
|
||||||
|
|
||||||
# SSH setup
|
# SSH setup
|
||||||
EXPOSE ${SSH_PORT}
|
# EXPOSE ${SSH_PORT}
|
||||||
CMD ["/usr/sbin/sshd", "-D"]
|
CMD ["/usr/sbin/sshd", "-D"]
|
||||||
@@ -41,7 +41,10 @@ EOT
|
|||||||
# Install base tools for compilation
|
# Install base tools for compilation
|
||||||
RUN <<EOT
|
RUN <<EOT
|
||||||
#!/bin/bash
|
#!/bin/bash
|
||||||
apt update && apt install -y --no-install-recommends \
|
apt-get update && apt-get install -y tzdata
|
||||||
|
ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
|
||||||
|
echo "Asia/Shanghai" > /etc/timezone
|
||||||
|
apt-get install -y --no-install-recommends \
|
||||||
build-essential \
|
build-essential \
|
||||||
autotools-dev \
|
autotools-dev \
|
||||||
libaio-dev \
|
libaio-dev \
|
||||||
@@ -70,17 +73,40 @@ apt update && apt install -y --no-install-recommends \
|
|||||||
pkg-config \
|
pkg-config \
|
||||||
cmake \
|
cmake \
|
||||||
bzip2 \
|
bzip2 \
|
||||||
|
curl \
|
||||||
|
bzip2 \
|
||||||
tar \
|
tar \
|
||||||
curl \
|
curl \
|
||||||
wget \
|
wget \
|
||||||
jq
|
jq \
|
||||||
|
openssh-client \
|
||||||
|
openssh-server \
|
||||||
|
htop jq \
|
||||||
|
libgl1-mesa-glx bash-completion \
|
||||||
|
iftop iotop ca-certificates
|
||||||
pip install pipx
|
pip install pipx
|
||||||
pipx install nvitop
|
pipx install nvitop
|
||||||
pipx ensurepath
|
pipx ensurepath
|
||||||
. ~/.bashrc
|
. ~/.bashrc
|
||||||
EOT
|
EOT
|
||||||
|
|
||||||
RUN echo "Check wget version" && wget --version
|
# SSH setup
|
||||||
|
RUN <<EOT
|
||||||
|
#!/bin/bash
|
||||||
|
mkdir ~/.ssh
|
||||||
|
printf "Host * \n ForwardAgent yes\nHost *\n StrictHostKeyChecking no" > ~/.ssh/config
|
||||||
|
cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
|
||||||
|
sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
|
||||||
|
sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
|
||||||
|
sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
|
||||||
|
sed -i 's/^\(\s*\)GSSAPIAuthentication yes/\1GSSAPIAuthentication no/' /etc/ssh/ssh_config
|
||||||
|
sed -i "s/^#Port 22/Port ${SSH_PORT}/" /etc/ssh/sshd_config
|
||||||
|
ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
|
||||||
|
cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
|
||||||
|
chmod 600 /root/.ssh/authorized_keys
|
||||||
|
mkdir /var/run/sshd
|
||||||
|
echo "root:${ROOT_PASSWD}" | chpasswd
|
||||||
|
EOT
|
||||||
|
|
||||||
# Install Modules for environment management
|
# Install Modules for environment management
|
||||||
COPY ./file/modules-5.4.0.tar.gz /root
|
COPY ./file/modules-5.4.0.tar.gz /root
|
||||||
@@ -192,14 +218,6 @@ make install
|
|||||||
echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
|
echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
|
||||||
EOT
|
EOT
|
||||||
|
|
||||||
# Install AmberTools and Amber
|
|
||||||
COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
|
|
||||||
RUN <<EOT
|
|
||||||
#!/bin/bash
|
|
||||||
tar -xjvf Amber24.tar.bz2
|
|
||||||
tar -xjvf AmberTools24.tar.bz2
|
|
||||||
EOT
|
|
||||||
|
|
||||||
# Install Boost
|
# Install Boost
|
||||||
COPY file/boost_1_86_0.tar.gz /root
|
COPY file/boost_1_86_0.tar.gz /root
|
||||||
ENV MODULEPATH=/opt/modulefiles/boost:$MODULEPATH
|
ENV MODULEPATH=/opt/modulefiles/boost:$MODULEPATH
|
||||||
@@ -233,32 +251,6 @@ echo "source /opt/intel/setvars.sh" >> ~/.bashrc
|
|||||||
echo "source /opt/intel/onemkl/setvars.sh" >> ~/.bashrc
|
echo "source /opt/intel/onemkl/setvars.sh" >> ~/.bashrc
|
||||||
EOT
|
EOT
|
||||||
|
|
||||||
# SSH setup
|
|
||||||
RUN <<EOT
|
|
||||||
#!/bin/bash
|
|
||||||
mkdir ~/.ssh
|
|
||||||
printf "Host * \n ForwardAgent yes\nHost *\n StrictHostKeyChecking no" > ~/.ssh/config
|
|
||||||
cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
|
|
||||||
sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
|
|
||||||
sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
|
|
||||||
sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
|
|
||||||
sed -i 's/^\(\s*\)GSSAPIAuthentication yes/\1GSSAPIAuthentication no/' /etc/ssh/ssh_config
|
|
||||||
sed -i "s/^#Port 22/Port ${SSH_PORT}/" /etc/ssh/sshd_config
|
|
||||||
ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
|
|
||||||
cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
|
|
||||||
chmod 600 /root/.ssh/authorized_keys
|
|
||||||
mkdir /var/run/sshd
|
|
||||||
echo "root:${ROOT_PASSWD}" | chpasswd
|
|
||||||
EOT
|
|
||||||
|
|
||||||
# Timezone setup
|
|
||||||
RUN <<EOT
|
|
||||||
#!/bin/bash
|
|
||||||
apt-get install -y tzdata
|
|
||||||
ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
|
|
||||||
echo "Asia/Shanghai" > /etc/timezone
|
|
||||||
EOT
|
|
||||||
|
|
||||||
# Install micromamba silently
|
# Install micromamba silently
|
||||||
WORKDIR /root
|
WORKDIR /root
|
||||||
ENV BIN_FOLDER=/usr/local/bin
|
ENV BIN_FOLDER=/usr/local/bin
|
||||||
@@ -284,6 +276,16 @@ RUN <<EOT
|
|||||||
git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
|
git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
|
||||||
EOT
|
EOT
|
||||||
|
|
||||||
|
# Install AmberTools and Amber
|
||||||
|
COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
|
||||||
|
RUN <<EOT
|
||||||
|
#!/bin/bash
|
||||||
|
tar -xjvf Amber24.tar.bz2
|
||||||
|
tar -xjvf AmberTools24.tar.bz2
|
||||||
|
EOT
|
||||||
|
|
||||||
|
# install mmgbsa
|
||||||
|
|
||||||
# Final cleanup
|
# Final cleanup
|
||||||
RUN <<EOT
|
RUN <<EOT
|
||||||
#!/bin/bash
|
#!/bin/bash
|
||||||
@@ -292,72 +294,3 @@ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
|
|||||||
rm -rf /root/modules-5.4.0 /root/fftw-${FFTW_VERSION} /root/ucx /root/ompi /root/plumed-${PLUMED_VERSION} /root/gromacs-${GROMACS_VERSION}
|
rm -rf /root/modules-5.4.0 /root/fftw-${FFTW_VERSION} /root/ucx /root/ompi /root/plumed-${PLUMED_VERSION} /root/gromacs-${GROMACS_VERSION}
|
||||||
rm -rf /root/Amber24.tar.bz2 /root/AmberTools24.tar.bz2 /root/boost_1_86_0.tar.gz
|
rm -rf /root/Amber24.tar.bz2 /root/AmberTools24.tar.bz2 /root/boost_1_86_0.tar.gz
|
||||||
EOT
|
EOT
|
||||||
|
|
||||||
# Stage 2: Runtime image
|
|
||||||
# FROM nvidia/cuda:${TAG_VERSION}
|
|
||||||
|
|
||||||
# ENV CUDA_HOME=/usr/local/cuda
|
|
||||||
# ENV PATH=$CUDA_HOME/bin:$PATH
|
|
||||||
# ENV LD_LIBRARY_PATH=$CUDA_HOME/lib64:/usr/local/plumed/lib:$LD_LIBRARY_PATH
|
|
||||||
# ENV CPATH=$CUDA_HOME/include:$CPATH
|
|
||||||
# ENV LIBRARY_PATH=$CUDA_HOME/lib64:$LIBRARY_PATH
|
|
||||||
# ARG SSH_PORT=2222
|
|
||||||
# WORKDIR /root
|
|
||||||
# SHELL ["/bin/bash", "-c"]
|
|
||||||
# ARG GROMACS_VERSION="2021.7"
|
|
||||||
# ARG PLUMED_VERSION="2.9.2"
|
|
||||||
|
|
||||||
# # Copy necessary files from build stage
|
|
||||||
# COPY --from=build-env /usr/local/fftw /usr/local/fftw
|
|
||||||
# COPY --from=build-env /usr/local/ucx /usr/local/ucx
|
|
||||||
# COPY --from=build-env /usr/local/openmpi /usr/local/openmpi
|
|
||||||
# COPY --from=build-env /usr/local/plumed /usr/local/plumed
|
|
||||||
# COPY --from=build-env /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
|
|
||||||
# COPY --from=build-env /opt/micromamba /opt/micromamba
|
|
||||||
# COPY --from=build-env /usr/local/bin/micromamba /usr/local/bin/micromamba
|
|
||||||
# COPY --from=build-env /root/.bashrc /root/.bashrc
|
|
||||||
# # COPY --from=build-env /root/.condarc /root/.condarc # Copy micromamba config file
|
|
||||||
# # COPY --from=build-env /root/.mambarc /root/.mambarc # Copy micromamba config file (if exists)
|
|
||||||
# COPY --from=build-env /opt/intel /opt/intel
|
|
||||||
# COPY --from=build-env /opt/intel/onemkl /opt/intel/onemkl
|
|
||||||
# COPY --from=build-env /opt/boost /opt/boost
|
|
||||||
# COPY --from=build-env /opt/modulefiles /opt/modulefiles
|
|
||||||
# COPY --from=build-env /root/.ssh /root/.ssh
|
|
||||||
# # COPY --from=build-env /etc/ssh/sshd_config /etc/ssh/sshd_config
|
|
||||||
# COPY --from=build-env /var/run/sshd /var/run/sshd
|
|
||||||
|
|
||||||
# # Set up micromamba environment
|
|
||||||
# RUN <<EOT
|
|
||||||
# #!/bin/bash
|
|
||||||
# # Add micromamba to PATH
|
|
||||||
# echo 'export PATH=/usr/local/bin:$PATH' >> /root/.bashrc
|
|
||||||
# # Initialize micromamba for bash
|
|
||||||
# eval "$(micromamba shell hook --shell )"
|
|
||||||
# /usr/local/bin/micromamba shell init --shell=bash --root-prefix=/opt/micromamba
|
|
||||||
# # Activate micromamba
|
|
||||||
# source /root/.bashrc
|
|
||||||
# micromamba self-update
|
|
||||||
# micromamba config append channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
|
|
||||||
# micromamba config append channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
|
|
||||||
# micromamba config append channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
|
|
||||||
# micromamba config append channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/linux-64/
|
|
||||||
# micromamba config append channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r
|
|
||||||
# micromamba config append channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2
|
|
||||||
# micromamba config append channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
|
|
||||||
# micromamba config append channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
|
|
||||||
# micromamba config append channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
|
|
||||||
# # Activate the PyAutoFEP environment
|
|
||||||
# micromamba activate PyAutoFEP
|
|
||||||
# mkdir -p ~/.pip
|
|
||||||
# cat << EOF > ~/.pip/pip.conf
|
|
||||||
# [global]
|
|
||||||
# index-url = https://mirrors.aliyun.com/pypi/simple/
|
|
||||||
|
|
||||||
# [install]
|
|
||||||
# trusted-host=mirrors.aliyun.com
|
|
||||||
# EOF
|
|
||||||
# EOT
|
|
||||||
|
|
||||||
# SSH setup
|
|
||||||
EXPOSE ${SSH_PORT}
|
|
||||||
CMD ["/usr/sbin/sshd", "-D"]
|
|
||||||
@@ -14,8 +14,8 @@ services:
|
|||||||
BUILDKIT_INLINE_CACHE: 1
|
BUILDKIT_INLINE_CACHE: 1
|
||||||
# env_file:
|
# env_file:
|
||||||
# - .env
|
# - .env
|
||||||
volumes:
|
# volumes:
|
||||||
- ./data:/data
|
# - ./data:/data
|
||||||
container_name: gromacs_amber_stage
|
container_name: gromacs_amber_stage
|
||||||
pull_policy: if_not_present
|
pull_policy: if_not_present
|
||||||
ulimits:
|
ulimits:
|
||||||
@@ -33,8 +33,8 @@ services:
|
|||||||
- NVIDIA_VISIBLE_DEVICES=all
|
- NVIDIA_VISIBLE_DEVICES=all
|
||||||
- NVIDIA_DRIVER_CAPABILITIES=compute,utility
|
- NVIDIA_DRIVER_CAPABILITIES=compute,utility
|
||||||
- TMPDIR=/var/tmp
|
- TMPDIR=/var/tmp
|
||||||
ports:
|
# ports:
|
||||||
- "53322:2222"
|
# - "53322:2222"
|
||||||
# network_mode: host
|
# network_mode: host
|
||||||
# command: ["/usr/sbin/sshd", "-D"]
|
# command: ["/usr/sbin/sshd", "-D"]
|
||||||
command: ["tail", "-f", "/dev/null"]
|
command: ["tail", "-f", "/dev/null"]
|
||||||
|
|||||||
@@ -14,8 +14,8 @@ services:
|
|||||||
BUILDKIT_INLINE_CACHE: 1
|
BUILDKIT_INLINE_CACHE: 1
|
||||||
# env_file:
|
# env_file:
|
||||||
# - .env
|
# - .env
|
||||||
volumes:
|
# volumes:
|
||||||
- ./data:/data
|
# - ./data:/data
|
||||||
container_name: gromacs_amber_staget
|
container_name: gromacs_amber_staget
|
||||||
pull_policy: if_not_present
|
pull_policy: if_not_present
|
||||||
ulimits:
|
ulimits:
|
||||||
@@ -33,8 +33,8 @@ services:
|
|||||||
- NVIDIA_VISIBLE_DEVICES=all
|
- NVIDIA_VISIBLE_DEVICES=all
|
||||||
- NVIDIA_DRIVER_CAPABILITIES=compute,utility
|
- NVIDIA_DRIVER_CAPABILITIES=compute,utility
|
||||||
- TMPDIR=/var/tmp
|
- TMPDIR=/var/tmp
|
||||||
ports:
|
# ports:
|
||||||
- "53322:2222"
|
# - "53322:2222"
|
||||||
# network_mode: host
|
# network_mode: host
|
||||||
# command: ["/usr/sbin/sshd", "-D"]
|
# command: ["/usr/sbin/sshd", "-D"]
|
||||||
command: ["tail", "-f", "/dev/null"]
|
command: ["tail", "-f", "/dev/null"]
|
||||||
|
|||||||
Reference in New Issue
Block a user