temp save

2025-01-18 21:42:09 +08:00
parent 8d7d1e766d
commit 085ebcb84f
4 changed files with 115 additions and 182 deletions
--- a/Dockerfile.gromacs_amber_stage
+++ b/Dockerfile.gromacs_amber_stage
@@ -22,26 +22,13 @@ ENV SSH_PORT=2222
 WORKDIR /root
 SHELL ["/bin/bash", "-c"]

-# Replace sources.list with Aliyun mirror
-RUN <<EOT
-#!/bin/bash
-cp /etc/apt/sources.list /etc/apt/sources.list_bak
-cat << EOF > /etc/apt/sources.list
-deb https://mirrors.aliyun.com/ubuntu/ jammy main restricted universe multiverse
-deb-src https://mirrors.aliyun.com/ubuntu/ jammy main restricted universe multiverse
-deb https://mirrors.aliyun.com/ubuntu/ jammy-security main restricted universe multiverse
-deb-src https://mirrors.aliyun.com/ubuntu/ jammy-security main restricted universe multiverse
-deb https://mirrors.aliyun.com/ubuntu/ jammy-updates main restricted universe multiverse
-deb-src https://mirrors.aliyun.com/ubuntu/ jammy-updates main restricted universe multiverse
-deb https://mirrors.aliyun.com/ubuntu/ jammy-backports main restricted universe multiverse
-deb-src https://mirrors.aliyun.com/ubuntu/ jammy-backports main restricted universe multiverse
-EOF
-EOT
-
 # Install base tools for compilation
 RUN <<EOT
 #!/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 \
    autotools-dev \
    libaio-dev \
@@ -70,29 +57,39 @@ apt update && apt install -y --no-install-recommends \
    pkg-config \
    cmake \
    bzip2 \
+    curl \
+    bzip2 \
    tar \
    curl \
    wget \
-    jq
+    jq \
+    openssh-client \
+    openssh-server \
+    htop jq \
+    libgl1-mesa-glx bash-completion \
+    iftop iotop ca-certificates
 pip install pipx
 pipx install nvitop
 pipx ensurepath
 . ~/.bashrc
 EOT

-RUN echo "Check wget version" && wget --version
-
-# Install Modules for environment management
-COPY ./file/modules-5.4.0.tar.gz /root
+# SSH setup
 RUN <<EOT
 #!/bin/bash
-tar zxvf modules-5.4.0.tar.gz
-cd modules-5.4.0
-./configure --prefix=/opt/modules --bindir=/opt/modules/bin --libdir=/opt/modules/lib --disable-libtclenvmodules
-make -j$(nproc)
-make install
-echo "source /opt/modules/init/profile.sh" >> /etc/profile
-echo "source /opt/modules/init/profile.sh" >> ~/.bashrc
+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 FFTW
@@ -192,14 +189,6 @@ make install
 echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
 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
 COPY file/boost_1_86_0.tar.gz /root
 ENV MODULEPATH=/opt/modulefiles/boost:$MODULEPATH
@@ -233,32 +222,6 @@ echo "source /opt/intel/setvars.sh" >> ~/.bashrc
 echo "source /opt/intel/onemkl/setvars.sh" >> ~/.bashrc
 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
 WORKDIR /root
 ENV BIN_FOLDER=/usr/local/bin
@@ -284,6 +247,16 @@ RUN <<EOT
 git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
 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
 RUN <<EOT
 #!/bin/bash
@@ -313,8 +286,8 @@ 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 /opt /opt
+COPY --from=build-env /usr/local/bin /usr/local/bin
 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)
@@ -323,12 +296,39 @@ 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 /etc/ssh/sshd_config /etc/ssh/sshd_config
 COPY --from=build-env /var/run/sshd /var/run/sshd
+COPY --from=build-env /root/.local /root/.local

 # Set up micromamba environment
 RUN <<EOT
 #!/bin/bash
+apt update && apt install -y --no-install-recommends tcl-dev \
+    gcc \
+    grep \
+    environment-modules \
+    tcl-devel \
+    vim \
+    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
+export HTTPS_PROXY="http://127.0.0.1:20171"
+export HTTP_PROXY="http://127.0.0.1:20171"
+wget https://sourceforge.net/projects/modules/files/Modules/modules-5.5.0/modules-5.5.0.tar.gz/download
+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
+make
+make install
 # Add micromamba to PATH
 echo 'export PATH=/usr/local/bin:$PATH' >> /root/.bashrc
 # Initialize micromamba for bash
@@ -359,5 +359,5 @@ EOF
 EOT

 # SSH setup
-EXPOSE ${SSH_PORT}
+# EXPOSE ${SSH_PORT}
 CMD ["/usr/sbin/sshd", "-D"]
--- a/Dockerfile.gromacs_amber_staget
+++ b/Dockerfile.gromacs_amber_staget
@@ -41,7 +41,10 @@ EOT
 # Install base tools for compilation
 RUN <<EOT
 #!/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 \
    autotools-dev \
    libaio-dev \
@@ -70,17 +73,40 @@ apt update && apt install -y --no-install-recommends \
    pkg-config \
    cmake \
    bzip2 \
+    curl \
+    bzip2 \
    tar \
    curl \
    wget \
-    jq
+    jq \
+    openssh-client \
+    openssh-server \
+    htop jq \
+    libgl1-mesa-glx bash-completion \
+    iftop iotop ca-certificates
 pip install pipx
 pipx install nvitop
 pipx ensurepath
 . ~/.bashrc
 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
 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
 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
 COPY file/boost_1_86_0.tar.gz /root
 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
 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
 WORKDIR /root
 ENV BIN_FOLDER=/usr/local/bin
@@ -284,6 +276,16 @@ RUN <<EOT
 git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
 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
 RUN <<EOT
 #!/bin/bash
@@ -291,73 +293,4 @@ apt-get clean
 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-${GROMACS_VERSION}
 rm -rf /root/Amber24.tar.bz2 /root/AmberTools24.tar.bz2 /root/boost_1_86_0.tar.gz
-EOT
-
-# Stage 2: Runtime image
-# FROM nvidia/cuda:${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"]
+EOT
--- a/docker-compose_amber_stage.yml
+++ b/docker-compose_amber_stage.yml
@@ -14,8 +14,8 @@ services:
        BUILDKIT_INLINE_CACHE: 1
    # env_file:
    #   - .env
-    volumes:
-      - ./data:/data
+    # volumes:
+    #   - ./data:/data
    container_name: gromacs_amber_stage
    pull_policy: if_not_present
    ulimits:
@@ -33,8 +33,8 @@ services:
      - NVIDIA_VISIBLE_DEVICES=all
      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
      - TMPDIR=/var/tmp
-    ports:
-      - "53322:2222" 
+    # ports:
+    #   - "53322:2222" 
    # network_mode: host
    # command: ["/usr/sbin/sshd", "-D"]
    command: ["tail", "-f", "/dev/null"]
--- a/docker-compose_amber_staget.yml
+++ b/docker-compose_amber_staget.yml
@@ -14,8 +14,8 @@ services:
        BUILDKIT_INLINE_CACHE: 1
    # env_file:
    #   - .env
-    volumes:
-      - ./data:/data
+    # volumes:
+    #   - ./data:/data
    container_name: gromacs_amber_staget
    pull_policy: if_not_present
    ulimits:
@@ -33,8 +33,8 @@ services:
      - NVIDIA_VISIBLE_DEVICES=all
      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
      - TMPDIR=/var/tmp
-    ports:
-      - "53322:2222" 
+    # ports:
+    #   - "53322:2222" 
    # network_mode: host
    # command: ["/usr/sbin/sshd", "-D"]
    command: ["tail", "-f", "/dev/null"]