commit 247fc2baf0daf4dec7e8554df9a761c370ff1592
Author: lingyuzeng <pylyzeng@gmail.com>
Date:   Mon Sep 9 20:36:26 2024 +0800

    add

diff --git a/Dockerfile b/Dockerfile
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+# syntax=docker/dockerfile:1
+FROM nvidia/cuda:12.3.1-devel-ubuntu22.04
+
+# 定义变量
+ARG FFTW_VERSION=3.3.10
+ARG GROMACS_VERSION=2023.2
+ARG INSTALL_DIR=/opt
+ARG GMX_INSTALL_PREFIX=${INSTALL_DIR}/software/gmx
+ARG CUDA_TOOLKIT_PATH=/usr/local/cuda
+ARG OPENMPI_PATH=${INSTALL_DIR}/software/openmpi
+
+# 使用 Here-docs 安装软件 openmpi 等
+RUN <<EOT 
+#!/bin/bash
+apt-get update 
+apt-get install -y cmake curl wget libpmix-dev openmpi-bin libopenmpi-dev
+mkdir -p ${INSTALL_DIR}/software 
+EOT
+
+#install fftw
+WORKDIR ${INSTALL_DIR}/software
+RUN <<EOF
+#!/bin/bash
+wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
+tar -xzvf fftw-${FFTW_VERSION}.tar.gz
+cd fftw-${FFTW_VERSION} 
+./configure --prefix=${INSTALL_DIR}/software/fftw --enable-sse2 --enable-avx --enable-float --enable-shared --enable-avx2 
+make install -j 
+echo 'export PATH=$PATH:${INSTALL_DIR}/software/fftw/bin' >> ~/.bashrc 
+echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${INSTALL_DIR}/software/fftw/lib' >> ~/.bashrc 
+EOF
+
+# install gromacs
+WORKDIR ${INSTALL_DIR}/software
+RUN <<EOF
+#!/bin/bash
+wget https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz 
+tar xfz gromacs-${GROMACS_VERSION}.tar.gz 
+cd gromacs-${GROMACS_VERSION} 
+mkdir build 
+cd build 
+echo 'export CMAKE_PREFIX_PATH=${INSTALL_DIR}/software/fftw' >> ~/.bashrc 
+cmake .. -DCMAKE_INSTALL_PREFIX=${GMX_INSTALL_PREFIX} -DGMX_USE_RDTSCP=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=${CUDA_TOOLKIT_PATH} -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON 
+make 
+make install -j8
+EOF
+
+ENV PATH="${GMX_INSTALL_PREFIX}/bin:${PATH}"
+
+# 设置容器启动时的默认命令
+CMD ["gmx_mpi"]
diff --git a/Dockerfile.gromacs b/Dockerfile.gromacs
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+++ b/Dockerfile.gromacs
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+# syntax=docker/dockerfile:1
+# NOTE: Building this image require's docker version >= 23.0.
+#
+# For reference:
+# - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
+ARG TAG_VERSION="12.4.1"
+FROM nvidia/cuda:${TAG_VERSION}-cudnn-devel-ubuntu22.04
+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"]
+
+# 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
+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
+# install pixi
+curl -fsSL https://pixi.sh/install.sh | bash
+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
+
+# 安装openmpi
+ENV MPI_HOME=/usr/local/openmpi
+ENV PATH=${MPI_HOME}/bin:/usr/bin:$PATH
+ENV LD_LIBRARY_PATH=/usr/local/cuda/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:$LD_LIBRARY_PATH
+RUN <<EOT
+#!/bin/bash
+apt update &&  apt install -y autoconf automake libtool flex
+/usr/bin/python3 -m pip install cython
+git clone --recursive https://github.com/open-mpi/ompi.git
+cd ompi
+git checkout main
+# make clean
+# make distclean
+./autogen.pl
+mkdir build
+cd build
+../configure --with-cuda=/usr/local/cuda --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-python=/usr/bin/python3
+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
+EOT
+
+# 安装plumed
+ARG PLUMED_VERSION="2.9.1"
+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="2022.5"
+ENV GROMACS_VERSION=${GROMACS_VERSION}
+ENV GROMACS_HOME=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
+ENV PATH=PATH=$GROMACS_HOME/bin:$PATH
+RUN <<EOT
+#!/bin/bash
+wget -c https://ftp.gromacs.org/gromacs/gromacs-${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-${PLUMED_VERSION} \
+         -DGMX_BUILD_OWN_FFTW=ON \
+         -DREGRESSIONTEST_DOWNLOAD=ON \
+         -DGMX_GPU=CUDA \
+         -DGMX_MPI=ON
+make -j$(nproc)
+make install 
+echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
+EOT
+
+RUN <<EOT
+#!/bin/bash
+apt-get clean && rm -rf /var/lib/apt/lists/*
+EOT
+
+EXPOSE 2222
+
+CMD ["/usr/sbin/sshd", "-D"]
diff --git a/README.md b/README.md
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+++ b/README.md
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+# gromacs_docker
+
+在容器中使用gpu需要安装：[nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html)
+
+运行命令：
+
+```shell
+docker run -it --net=host --gpus all --name 容器名 -e NVIDIA_DRIVER_CAPABILITIES=compute,utility -e NVIDIA_VISIBLE_DEVICES=all 镜像名
+```
+
+首次使用报错：
+
+```shell
+docker: Error response from daemon: could not select device driver “” with capabilities: [[gpu]].
+```
+
+解决办法：
+
+```shell
+sudo curl -s -L https://nvidia.github.io/nvidia-container-runtime/gpgkey | \
+  sudo apt-key add -
+distribution=$(. /etc/os-release;echo $ID$VERSION_ID)
+sudo curl -s -L https://nvidia.github.io/nvidia-container-runtime/$distribution/nvidia-container-runtime.list | \
+  sudo tee /etc/apt/sources.list.d/nvidia-container-runtime.list
+sudo apt-get update
+
+sudo apt-get install nvidia-container-runtime
+```
+
+02 验证执行下列命令：
+
+```shell
+which nvidia-container-runtime
+```
+
+输出 /usr/bin/nvidia-container-runtime，表示安装成功。
+03 docker 使用:
+
+```shell
+docker run -it --gpus all **
+```
+
+此时，设置使用设备上全部的显卡。
+
+目前尚不支持debian12
\ No newline at end of file
diff --git a/docker-compose.yml b/docker-compose.yml
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+version: '3.8'
+
+services:
+  gromacs:
+    build: 
+      context: .
+      dockerfile: Dockerfile.gromacs
+      args: 
+        CACHEBUST: 1
+        TAG_VERSION: "12.4.1"
+        PLUMED_VERSION: "2.9.1"
+        FFTW_VERSION: "3.3.10"
+        BUILDKIT_INLINE_CACHE: 1
+    # env_file:
+    #   - .env
+    # volumes:
+    #   - ./hostfile:/hostfile
+    container_name: gromacs
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    restart: unless-stopped
+    image: hotwa/gromacs:test
+    privileged: true
+    cap_add:
+      - ALL
+      - CAP_SYS_PTRACE
+    shm_size: '64gb'
+    # 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
+      # - 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:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]