add amber

Dockerfile.amber_test

@@ -0,0 +1,39 @@
+FROM nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04
+# 将 <CUDA_VERSION> 替换为您的目标 CUDA 版本
+# 将 <OS_VERSION> 替换为您的目标操作系统版本，例如 ubuntu20.04
+
+# 安装必要的编译器和库
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    cmake \
+    git \
+    bzip2-devel cmake3 gcc-gfortran g++ lzip tcl-devel zlib libzip-devel 
+
+# 设置工作目录
+WORKDIR /amber
+
+# 复制 Amber 源代码到容器中
+COPY AmberTools24.tar.bz2 /amber/
+COPY Amber24.tar.bz2 /amber/  # 如果您已获得 Amber24 许可证
+
+# 解压 Amber 源代码
+RUN tar xvfj AmberTools24.tar.bz2 && \
+    tar xvfj Amber24.tar.bz2 # 如果您已获得 Amber24 许可证
+
+# 进入 AmberTools24 源代码目录
+WORKDIR /amber/amber24_src/build
+
+# 使用 cmake 配置 Amber 构建选项
+RUN ./run_cmake -DMPI=TRUE -DCUDA=TRUE \
+    -DCUDA_ARCH=native,sm_86,sm_75,sm_87
+    # ... 其他 cmake 选项
+
+# 构建 Amber
+RUN make install
+
+# 设置 Amber 环境变量
+ENV AMBERHOME /amber/amber24
+ENV PATH $AMBERHOME/bin:$PATH
+
+# 测试 Amber 安装 (可选)
+RUN cd $AMBERHOME && make test.parallel

Dockerfile.gromacs_amber

@@ -3,8 +3,13 @@
 #
 # For reference:
 # - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
-ARG TAG_VERSION="12.4.1"
-FROM nvidia/cuda:${TAG_VERSION}-cudnn-devel-ubuntu22.04
+ARG TAG_VERSION="12.4.1-cudnn-devel-ubuntu22.04"
+FROM nvidia/cuda:${TAG_VERSION}
+ENV CUDA_HOME=/usr/local/cuda
+ENV PATH=$CUDA_HOME/bin:$PATH
+ENV LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH
+ENV CPATH=$CUDA_HOME/include:$CPATH
+ENV LIBRARY_PATH=$CUDA_HOME/lib64:$LIBRARY_PATH
 ARG HTTP_PROXY
 ARG HTTPS_PROXY
 ENV http_proxy=${HTTP_PROXY}
@@ -17,6 +22,27 @@ ENV SSH_PORT=2222
 WORKDIR /root
 SHELL ["/bin/bash", "-c"]
 
+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-proposed main restricted universe multiverse
+# deb-src https://mirrors.aliyun.com/ubuntu/ jammy-proposed 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
+
 # base tools
 RUN <<EOT
 #!/bin/bash
@@ -60,7 +86,6 @@ echo "Asia/Shanghai" > /etc/timezone
 # curl -fsSL https://pixi.sh/install.sh | bash
 EOT
 
-ENV CUDA_HOME=/usr/local/cuda
 ENV PATH=/opt/modules/bin:$PATH
 ENV LIBRARY_PATH=/opt/modules/lib:$LIBRARY_PATH
 COPY ./file/modules-5.4.0.tar.gz /root
@@ -101,18 +126,18 @@ EOT
 # https://openucx.readthedocs.io/en/master
 # Running in Docker containers
 # https://openucx.readthedocs.io/en/master/running.html#running-in-docker-containers
-ENV UCX_HOME=/usr/local/ucx
-ENV PATH=${CUDA_HOME}/bin:${UCX_HOME}/bin:$PATH
-ENV LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${UCX_HOME}/lib:$LD_LIBRARY_PATH
+ENV UCX_PREFIX=/usr/local/ucx
+ENV PATH=$UCX_PREFIX/bin:$PATH
+ENV LD_LIBRARY_PATH=$UCX_PREFIX/lib:$LD_LIBRARY_PATH
+ENV CPATH=$UCX_PREFIX/include:$CPATH
+ENV LIBRARY_PATH=$UCX_PREFIX/lib:$LIBRARY_PATH
 RUN <<EOT
 #!/bin/bash
 # 启用调试信息
 sudo apt update
-sudo apt -y install gdb valgrind
-sudo apt-get update
-sudo apt-get install -y build-essential libnuma-dev pkg-config libfuse3-dev
+sudo apt -y install gdb valgrind autoconf build-essential libnuma-dev pkg-config libfuse3-dev automake libtool flex gfortran libibverbs-dev rdma-core
 # sudo apt install -y openmpi-bin openmpi-common openmpi-doc openmpi-debug libopenmpi-dev
-# sudo apt install -y libucx0-dbg libucs0-dbg libucm0-dbg libuct0-dbg libibverbs1-dbg librdmacm1-dbg libmlx5-1-dbg
+sudo apt install -y libucx0-dbg libucs0-dbg libucm0-dbg libuct0-dbg libibverbs1-dbg librdmacm1-dbg libmlx5-1-dbg
 git clone https://github.com/openucx/ucx.git
 cd ucx
 # git checkout v1.15.0
@@ -134,10 +159,10 @@ cd build
 # --with-dc \
 # --with-dm \
 # --with-verbs \
-# --with-go=/usr/local/go 
-# --with-mlx5 
 ../contrib/configure-release --prefix=${UCX_HOME} \
 --with-cuda=/usr/local/cuda \
+--with-mlx5 \
+--with-avx \
 --with-rc \
 --with-ud \
 --with-dc \
@@ -153,9 +178,8 @@ make install
 # 检查 UCX 进程
 # mpirun -np 2 -mca pml ucx -x UCX_NET_DEVICES=mlx5_0:1 ./your_mpi_program
 # CUDA support check
-ucx_info -c
-ucx_info -d
-# ompi_info | grep ucx
+# ucx_info -c
+# ucx_info -d
 EOT
 
 # 安装openmpi

Dockerfile.gromacs_amber_stage

@@ -0,0 +1,425 @@
+# syntax=docker/dockerfile:1.3-labs
+# NOTE: Building this image require's docker version >= 23.0.
+#
+# For reference:
+# - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
+ARG TAG_VERSION="12.4.1-cudnn-devel-ubuntu22.04"
+FROM nvidia/cuda:${TAG_VERSION} as apptainerbuilder
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ENV http_proxy=${HTTP_PROXY}
+ENV https_proxy=${HTTPS_PROXY}
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+# 安装必需的包
+RUN apt-get update && apt-get install -y \
+    wget \
+    gcc \
+    git \
+    libc-dev \
+    make \
+    bash \
+    linux-headers-generic \
+    libseccomp-dev \
+    libssl-dev \
+    libuuid1 \
+    uuid-dev \
+    pkg-config \
+    && rm -rf /var/lib/apt/lists/*
+
+# 安装 Go
+ARG GO_VERSION="1.21.13"
+RUN wget https://golang.org/dl/go${GO_VERSION}.linux-amd64.tar.gz && \
+    tar -C /usr/local -xzf go${GO_VERSION}.linux-amd64.tar.gz && \
+    rm go${GO_VERSION}.linux-amd64.tar.gz
+
+# 设置 Go 环境变量
+ENV PATH="/usr/local/go/bin:${PATH}"
+
+# 构建 Apptainer
+ARG APPTAINER_COMMITISH="main"
+ARG MCONFIG_OPTIONS="--with-suid"
+WORKDIR /go/src/github.com/apptainer
+RUN git clone https://github.com/apptainer/apptainer.git \
+    && cd apptainer \
+    && git checkout "$APPTAINER_COMMITISH" \
+    && ./mconfig $MCONFIG_OPTIONS -p /usr/local/apptainer \
+    && cd builddir \
+    && make \
+    && make install
+
+# 清理
+RUN apt-get remove -y wget gcc git && \
+    apt-get autoremove -y && \
+    apt-get clean
+
+FROM nvidia/cuda:${TAG_VERSION}
+# 复制 Apptainer 和 Go
+COPY --from=apptainerbuilder /usr/local/apptainer /usr/local/apptainer
+COPY --from=apptainerbuilder /usr/local/go /usr/local/go
+ENV CUDA_HOME=/usr/local/cuda
+ENV PATH=$CUDA_HOME/bin:$PATH
+ENV LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH
+ENV CPATH=$CUDA_HOME/include:$CPATH
+ENV LIBRARY_PATH=$CUDA_HOME/lib64:$LIBRARY_PATH
+ENV GO_PATH="/usr/local/go"
+ENV PATH="/usr/local/apptainer/bin:${GO_PATH}/bin:$PATH"
+ENV APPTAINER_TMPDIR="/tmp/tmp-apptainer"
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ENV http_proxy=${HTTP_PROXY}
+ENV https_proxy=${HTTPS_PROXY}
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG ROOT_PASSWD="root"
+ENV ROOT_PASSWD=${ROOT_PASSWD}
+ENV SSH_PORT=2222
+WORKDIR /root
+SHELL ["/bin/bash", "-c"]
+
+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-proposed main restricted universe multiverse
+# deb-src https://mirrors.aliyun.com/ubuntu/ jammy-proposed 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
+
+# base tools
+RUN <<EOT
+#!/bin/bash
+apt-get update
+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 screen
+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
+add-apt-repository ppa:git-core/ppa -y
+apt-get install -y git libnuma-dev wget
+pip install pipx
+pipx install nvitop
+pipx ensurepath 
+. ~/.bashrc
+# Configure SSH for password and public key authentication
+mkdir ~/.ssh
+# 创建或覆盖 SSH 配置文件 ~/.ssh/config
+# - Host *: 针对所有主机的通用配置
+# - 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
+# - 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）
+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
+sudo sed -i "s/#   Port 22/Port ${SSH_PORT}/" /etc/ssh/ssh_config
+ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
+cat ~/.ssh/id_rsa.pub >> ~/.ssh/auth
+cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys
+cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys2
+chmod 600 /root/.ssh/authorized_keys
+chmod 600 /root/.ssh/authorized_keys2
+mkdir /var/run/sshd
+echo "root:${ROOT_PASSWD}" | chpasswd
+mkdir -p ~/.pip
+# timezone
+apt-get install -y tzdata
+ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
+echo "Asia/Shanghai" > /etc/timezone
+# install pixi
+# curl -fsSL https://pixi.sh/install.sh | bash
+EOT
+
+ENV PATH=/opt/modules/bin:$PATH
+ENV LIBRARY_PATH=/opt/modules/lib:$LIBRARY_PATH
+COPY ./file/modules-5.4.0.tar.gz /root
+## install modules to manage environment variables download from https://modules.sourceforge.net/
+# usage: https://nscc.mrzhenggang.com/user-manual/config-env-with-module
+RUN <<EOT
+#!/bin/bash
+apt-get update && apt-get install -y tcl
+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 --with-tclsh=/usr/bin/tclsh
+./configure --prefix=/opt/modules --bindir=/opt/modules/bin --libdir=/opt/modules/lib --disable-libtclenvmodules
+make -j$(nproc)
+make install
+echo "source /opt/modules/init/profile.sh" >> /etc/profile
+echo "source /opt/modules/init/profile.sh" >> ~/.bashrc
+# /opt/modules/bin/modulecmd
+EOT
+
+ARG FFTW_VERSION="3.3.10"
+ENV FFTW_VERSION=${FFTW_VERSION}
+ENV PATH=/usr/local/fftw:$PATH
+# 安装fftw
+RUN <<EOT
+#!/bin/bash
+wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
+tar zxvf fftw-${FFTW_VERSION}.tar.gz
+cd fftw-${FFTW_VERSION}
+./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
+make -j$(nproc)
+make install
+EOT
+
+# install ucx
+# https://github.com/openucx/ucx
+# OpenMPI and OpenSHMEM installation with UCX
+# https://github.com/openucx/ucx/wiki/OpenMPI-and-OpenSHMEM-installation-with-UCX
+# https://openucx.readthedocs.io/en/master
+# Running in Docker containers
+# https://openucx.readthedocs.io/en/master/running.html#running-in-docker-containers
+ENV UCX_PREFIX=/usr/local/ucx
+ENV PATH=$UCX_PREFIX/bin:$PATH
+ENV LD_LIBRARY_PATH=$UCX_PREFIX/lib:$LD_LIBRARY_PATH
+ENV CPATH=$UCX_PREFIX/include:$CPATH
+ENV LIBRARY_PATH=$UCX_PREFIX/lib:$LIBRARY_PATH
+RUN <<EOT
+#!/bin/bash
+# 启用调试信息
+sudo apt update
+sudo apt -y install gdb valgrind autoconf build-essential libnuma-dev pkg-config libfuse3-dev automake libtool flex gfortran libibverbs-dev rdma-core
+# sudo apt install -y openmpi-bin openmpi-common openmpi-doc openmpi-debug libopenmpi-dev
+sudo apt install -y libucx0-dbg libucs0-dbg libucm0-dbg libuct0-dbg libibverbs1-dbg librdmacm1-dbg libmlx5-1-dbg
+git clone https://github.com/openucx/ucx.git
+cd ucx
+# git checkout v1.15.0
+git checkout master
+./autogen.sh
+mkdir build
+cd build
+# make clean
+# make distclean
+# 性能优化配置 ../contrib/configure-release --prefix=/usr/local/ucx --with-cuda=${CUDA_HOME}
+# 调试/开发配置 ../contrib/configure-devel --prefix=/usr/local/ucx --with-cuda=${CUDA_HOME}
+# default ../configure --prefix=/usr/local/ucx --with-cuda=${CUDA_HOME}
+# ../contrib/configure-release --prefix=${UCX_HOME} --with-cuda=${CUDA_HOME} --with-gdrcopy=/usr/local/gdrcopy
+# ../contrib/configure-release --prefix=/usr/local/ucx \
+# --with-cuda= /usr/local/cuda-12.5 \
+# --with-mlx5 \
+# --with-rc \
+# --with-ud \
+# --with-dc \
+# --with-dm \
+# --with-verbs \
+../contrib/configure-release --prefix=${UCX_HOME} \
+--with-cuda=/usr/local/cuda \
+--with-go=/usr/local/go \
+--with-mlx5 \
+--with-avx \
+--with-rc \
+--with-ud \
+--with-dc \
+--with-dm \
+--with-verbs
+make -j$(nproc)
+make install
+# ucx_info -a
+# 测试性能
+# ucx_perftest -d <device> -t bw -p <protocol> -n <num_iterations>
+# 测试 UCX 读取配置
+# ucx_read_profile
+# 检查 UCX 进程
+# mpirun -np 2 -mca pml ucx -x UCX_NET_DEVICES=mlx5_0:1 ./your_mpi_program
+# CUDA support check
+# ucx_info -c
+# ucx_info -d
+EOT
+
+# 安装openmpi
+ENV MPI_HOME=/usr/local/openmpi
+ENV PATH=${MPI_HOME}/bin:/usr/bin:$PATH
+ENV LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${MPI_HOME}/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
+ENV LIBRARY_PATH=/usr/local/cuda/lib64:${LIBRARY_PATH}
+ENV CPATH=/usr/local/cuda/include:${MPI_HOME}/include:${CUDA_HOME}/include:$CPATH
+# export C_INCLUDE_PATH=/usr/local/cuda/include:$C_INCLUDE_PATH
+# export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
+# export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
+RUN <<EOT
+#!/bin/bash
+apt update &&  apt install -y autoconf automake libtool flex gfortran
+/usr/bin/python3 -m pip install cython
+git clone --recursive https://github.com/open-mpi/ompi.git
+cd ompi
+git checkout main
+# make clean
+# make distclean
+./autogen.pl
+mkdir build
+cd build
+# ../configure --with-cuda=/usr/local/cuda --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-python=/usr/bin/python3 FC=gfortran
+# ../configure FC=gfortran PYTHON=/usr/bin/python3 --with-cuda=/usr/local/cuda --with-cuda-libdir=/usr/local/cuda/lib64 --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-ucx=${UCX_HOME}
+../configure FC=gfortran PYTHON=/usr/bin/python3 --with-cuda=/usr/local/cuda --with-cuda-libdir=/usr/local/cuda/lib64 --enable-python-bindings \
+ --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-ucx=${UCX_HOME} --enable-mca-dso=btl-smcuda,rcache-rgpusm,rcache-gpusm,accelerator-cuda --enable-mca-no-build=btl-uct --without-hcoll
+make -j$(nproc)
+make install
+# 验证CUDA支持
+cat <<EOF > ./test_mpi_cuda.cu
+#include <mpi.h>
+#include <cuda_runtime.h>
+#include <stdio.h>
+
+__global__ void hello_cuda() {
+    printf("Hello from CUDA kernel! Thread id: %d\n", threadIdx.x);
+}
+
+int main(int argc, char **argv) {
+    MPI_Init(&argc, &argv);
+
+    int rank;
+    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+
+    printf("Hello from MPI process %d!\n", rank);
+
+    // Launch CUDA kernel
+    hello_cuda<<<1, 10>>>();
+    cudaDeviceSynchronize();  // Wait for the CUDA kernel to finish
+
+    MPI_Finalize();
+    return 0;
+}
+EOF
+nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/include -L${MPI_HOME}/lib -lcudart -lmpi
+# mpirun --allow-run-as-root -np 2 ./test_mpi_cuda
+ompi_info | grep "MPI extensions"
+EOT
+
+# 安装plumed
+ARG PLUMED_VERSION="2.9.2"
+ENV PLUMED_VERSION=${PLUMED_VERSION}
+ENV LD_LIBRARY_PATH=/usr/local/plumed/lib:$LD_LIBRARY_PATH
+ENV PATH=/usr/local/plumed:/usr/local/plumed/bin:$PATH
+RUN <<EOT
+#!/bin/bash
+# git clone https://github.com/plumed/plumed2
+# cd plumed2
+# git checkout v${PLUMED_VERSION}
+curl -L -o plumed-${PLUMED_VERSION}.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_VERSION}/plumed-${PLUMED_VERSION}.tgz
+tar zxvf plumed-${PLUMED_VERSION}.tar.gz
+cd plumed-${PLUMED_VERSION}
+./configure --prefix=/usr/local/plumed
+make -j$(nproc)
+make install 
+EOT
+
+# 安装gromacs
+ARG GROMACS_VERSION="2021.7"
+ENV GROMACS_VERSION=${GROMACS_VERSION}
+ENV GROMACS_HOME=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
+ENV PATH=PATH=$GROMACS_HOME/bin:$PATH
+ARG CUDA_ARCH="75;86;89"
+ENV CUDA_ARCH=${CUDA_ARCH}
+RUN <<EOT
+#!/bin/bash
+wget -c https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz
+tar zxvf gromacs-${GROMACS_VERSION}.tar.gz
+cd gromacs-${GROMACS_VERSION}
+### patch the plumed
+# plumed-patch -p
+plumed-patch -p -e gromacs-${GROMACS_VERSION}
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} \
+         -DGMX_BUILD_OWN_FFTW=ON \
+         -DREGRESSIONTEST_DOWNLOAD=ON \
+         -DGMX_GPU=CUDA \
+         -DGMX_CUDA_TARGET_COMPUTE="75;86;89" \
+         -DGMX_CUDA_TARGET_SM="75;86;89" \
+         -DGMX_MPI=ON
+make -j$(nproc)
+make install 
+echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
+EOT
+
+# PyAutoFEP install support version: GROMACS 2021.7
+# GROMACS 2022.5 和 2023 中遇到的“排除原子距离超过截断距离”的问题，确保模拟的稳定性和自由能计算的收敛性。
+# https://github.com/luancarvalhomartins/PyAutoFEP/blob/master/docs/Manual.pdf
+# https://github.com/luancarvalhomartins/PyAutoFEP/tree/master/docs/tutorial01
+ENV CPLUS_INCLUDE_PATH=/usr/include/openbabel3
+ENV LIBRARY_PATH=/usr/lib:/usr/local/lib:${LIBRARY_PATH}
+RUN <<EOT
+#!/bin/bash
+sudo apt-get update
+sudo apt-get install openbabel libopenbabel-dev -y
+sudo apt-get install swig -y
+sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
+/usr/bin/python3 -m pip install ipython rdkit "networkx>2.0,<3.0" alchemlyb==0.6.0 pymbar==3.0.5 openbabel>3.0.0 matplotlib numpy biopython mdanalysis pytest packaging 
+# or openbabel use 2.4.1
+git clone https://github.com/luancarvalhomartins/PyAutoFEP.git 
+EOT
+
+COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
+COPY file/l_HPCKit_p_2024.2.1.79_offline.sh file/l_onemkl_p_2024.2.2.17_offline.sh /root
+COPY file/boost_1_86_0.tar.gz /root
+ENV DOWNLOAD_MINICONDA="False"
+# install HPCKit and oneMKL
+RUN <<EOT
+#!/bin/bash
+chmod +x l_HPCKit_p_2024.2.1.79_offline.sh
+./l_HPCKit_p_2024.2.1.79_offline.sh -a --silent --eula accept --install-dir /opt/intel
+chmod +x l_onemkl_p_2024.2.2.17_offline.sh
+./l_onemkl_p_2024.2.2.17_offline.sh -a --silent --eula accept --install-dir /opt/intel/onemkl
+# echo "source /opt/intel/setvars.sh" >> /etc/profile
+# echo "source /opt/intel/onemkl/setvars.sh" >> /etc/profile
+echo "source /opt/intel/setvars.sh" >> ~/.bashrc
+echo "source /opt/intel/onemkl/setvars.sh" >> ~/.bashrc
+mkdir -p /opt/modulefiles/intel
+chmod +x /opt/intel/setvars.sh
+chmod +x /opt/intel/onemkl/setvars.sh
+# curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+# echo  "source $HOME/.cargo/env" >> ~/.bashrc
+# cargo install modenv
+EOT
+# install ambertools
+ENV MODULEPATH=/opt/modulefiles/boost:$MODULEPATH
+RUN <<EOT
+#!/bin/bash
+python3 -m pip install numpy scipy matplotlib cython setuptools
+# install Boost from https://www.boost.org/users/download/
+tar zxvf boost_1_86_0.tar.gz
+cd boost_1_86_0
+./bootstrap.sh --prefix=/opt/boost --with-libraries=all --with-toolset=gcc
+echo "using mpi : /usr/local/openmpi/bin/mpicxx ;" >> project-config.jam
+# # echo "using mpi : /opt/intel/mpi/2021.13/bin/mpicxx ;" >> project-config.jam
+# ./b2 -j$(nproc) --layout=tagged link=static,shared threading=multi install
+# mkdir -p /opt/modulefiles/boost
+# use modulefile to load boost command is: 
+# module load boost/1.86.0-openmpi-5.1.0a1 | module list | module avail
+cat << EOF > /opt/modulefiles/boost/1.86.0-openmpi-5.1.0a1
+#%Module1.0
+set prefix /opt/boost
+
+# 设置库路径和头文件路径，方便编译器找到 Boost
+prepend-path LD_LIBRARY_PATH \$prefix/lib
+prepend-path CPATH \$prefix/include
+prepend-path LIBRARY_PATH \$prefix/lib
+prepend-path PATH \$prefix/bin
+EOF
+# 解压 Amber24
+tar -xjvf Amber24.tar.bz2
+# 解压 AmberTools24
+tar -xjvf AmberTools24.tar.bz2
+# 清理解压后的 .tar.bz2 文件（可选）
+# rm Amber24.tar.bz2 AmberTools24.tar.bz2
+EOT
+
+RUN <<EOT
+#!/bin/bash
+apt-get clean && rm -rf /var/lib/apt/lists/*
+EOT
+
+EXPOSE 2222
+
+CMD ["/usr/sbin/sshd", "-D"]

docker-compose_amber.yml

@@ -7,7 +7,7 @@ services:
       dockerfile: Dockerfile.gromacs_amber
       args: 
         CACHEBUST: 1
-        TAG_VERSION: "12.4.1"
+        TAG_VERSION: "12.4.1-cudnn-devel-ubuntu22.04"
         PLUMED_VERSION: "2.9.1"
         FFTW_VERSION: "3.3.10"
         BUILDKIT_INLINE_CACHE: 1
@@ -15,7 +15,7 @@ services:
     #   - .env
     volumes:
       - ./data:/data
-    container_name: gromacs
+    container_name: gromacs_amber
     pull_policy: if_not_present
     ulimits:
       memlock:
@@ -28,24 +28,12 @@ services:
       - ALL
       - CAP_SYS_PTRACE
     shm_size: '16gb'
-    # devices:
-    #   - /dev/infiniband/rdma_cm
-    #   - /dev/infiniband/uverbs0
-    #   - /dev/infiniband/uverbs1
-    #   - /dev/infiniband/uverbs2
-    #   - /dev/infiniband/uverbs3
-    #   - /dev/infiniband/uverbs4
-    #   - /dev/infiniband/uverbs5
-    #   - /dev/infiniband/uverbs6
-    #   - /dev/infiniband/uverbs7
-    #   - /dev/infiniband/uverbs8
     environment:
       - NVIDIA_VISIBLE_DEVICES=all
       - NVIDIA_DRIVER_CAPABILITIES=compute,utility
       - TMPDIR=/var/tmp
     ports:
       - "53322:2222" 
-      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
     # network_mode: host
     command: ["/usr/sbin/sshd", "-D"]
     deploy:

docker-compose_amber_stage.yml

@@ -0,0 +1,45 @@
+version: '3.8'
+
+services:
+  gromacs:
+    build: 
+      context: .
+      dockerfile: Dockerfile.gromacs_amber_stage
+      args: 
+        CACHEBUST: 1
+        TAG_VERSION: "12.4.1-cudnn-devel-ubuntu22.04"
+        PLUMED_VERSION: "2.9.1"
+        FFTW_VERSION: "3.3.10"
+        BUILDKIT_INLINE_CACHE: 1
+    # env_file:
+    #   - .env
+    volumes:
+      - ./data:/data
+    container_name: gromacs_amber_stage
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    restart: unless-stopped
+    image: hotwa/gromacs:amber
+    privileged: true
+    cap_add:
+      - ALL
+      - CAP_SYS_PTRACE
+    shm_size: '16gb'
+    environment:
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
+      - TMPDIR=/var/tmp
+    ports:
+      - "53322:2222" 
+    # network_mode: host
+    command: ["/usr/sbin/sshd", "-D"]
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]