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gromacs_docker/Dockerfile.gromacs_amber
root a977029c82 add amber
2024-10-23 21:06:48 +08:00

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# 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:${TAG_VERSION}
ENV CUDA_HOME=/usr/local/cuda
ENV PATH=$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}
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=${UCX_HOME} \
--with-cuda=/usr/local/cuda \
--with-mlx5 \
--with-avx \
--with-rc \
--with-ud \
--with-dc \
--with-dm \
--with-verbs
make -j$(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"]
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