Rocky Linux 9.4 系统以及计算软件安装

弃用Windows安装Rocky Linux 9.4

Rocky Linux 安装图解（替代centos）服务器+桌面-优快云博客

【部署笔记-Rocky Linux】Rocky Linux 系统安装

Rocky Linux 9 从入门到精通002 — 系统安装 – Rocky Linux

Rocky Linux 9 从入门到精通003 — 网络配置（基础篇） – Rocky Linux

安装CUDA驱动

1. 按照教程Rocky Linux 9 AI 系列 002 — 离线安装 NVIDIA 闭源驱动 – Rocky Linux 到安装驱动出现报错信息

[root@localhost software]# ./NVIDIA-Linux-x86_64-550.120.run
Verifying archive integrity... OK
Uncompressing NVIDIA Accelerated Graphics Driver for Linux-x86_64 550.120Extraction failed.

 2. 解决

dnf update && dnf upgrade -y
yum -y install gcc pciutils
yum -y install gcc-c++
yum -y install make
yum -y install binutils wget
yum -y install kernel-devel dkms
yum install epel-release #安装epel源
yum install libglvnd-devel.x86_64

# 禁用nouveau
echo -e "blacklist nouveau\noptions nouveau modeset=0" > /etc/modprobe.d/blacklist.conf
# 备份和重建 IMG
mv /boot/initramfs-$(uname -r).img /boot/initramfs-$(uname -r).img.bak
dracut /boot/initramfs-$(uname -r).img $(uname -r)
rpm --import https://www.elrepo.org/RPM-GPG-KEY-elrepo.org #添加 repo 源
systemctl set-default multi-user.target # 进入多用户模式
reboot #重启

3. 安装CUDA Toolkit 12.4

CUDA Toolkit Archive | NVIDIA Developer   CUDA下载地址

wget https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_550.54.14_linux.run
sudo sh cuda_12.4.0_550.54.14_linux.run

4. 添加变量到.bashrc文件

# CUDA
export PATH=/usr/local/cuda-12.4/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-12.4/lib64:$LD_LIBRARY_PATH

 source .bashrc

nvcc -V

安装GPU加速版Gromacs2024.0

辅助Gromacs 2018.8的安装参考GROMACS的安装方法（含全程视频演示） - 思想家公社的门口：量子化学·分子模拟·二次元

出现Cmake报错

CMake Error at /usr/share/cmake/Modules/CMakeDetermineCUDACompiler.cmake:603 (message): Failed to detect a default CUDA architecture. Compiler output: Call Stack (most recent call first): cmake/gmxManageCuda.cmake:116 (enable_language) CMakeLists.txt:699 (include)

解决

sudo yum install cmake3 gcc gcc-c++
sudo yum install python3-devel
sudo yum install python3-pip
pip3 install sphinx pygments
sudo mkdir build
cd build
sudo cmake3 .. -DCMAKE_INSTALL_PREFIX=/opt/gmx2024.0 -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.4 -DCUDA_ARCH_BIN=86  -DCUDA_HOST_COMPILER=/usr/bin/gcc -DCMAKE_CUDA_ARCHITECTURES=86 -DCMAKE_CUDA_COMPILER=/usr/local/cuda-12.4/bin/nvcc

# GeForce RTX 3080 Ti，CUDA 架构是 8.6，因此需要使用 CUDA_ARCH_BIN=86

 其他计算软件安装

http://bbs.keinsci.com/thread-43105-1-1.html

安装虚拟机

1. 在 Rocky Linux 9 上安装 VMware Workstation/Player 16

2. 在 Rocky Linux 9/AlmaLinux 9 上安装 VirtualBox 7.0

按照教程安装Virtualbox 7.0 扩展包报错

解决 

sudo wget https://download.virtualbox.org/virtualbox/7.0.20/Oracle_VM_VirtualBox_Extension_Pack-7.0.20.vbox-extpack

由于安装了Minimal版本，无法启动Virtualbox图形界面。

解决方法：安装Gnome桌面或者使用MobaXterm 的 X11 转发，在 SSH 会话中启动 VirtualBox

3. 如何在 Rocky Linux 9 上安装 Gnome 桌

安装Amber24

参考教程：Amber22和AmberTools23的编译 - 分子模拟 (Molecular Modeling) - 计算化学公社

1. 下载Amber24和AmberTools24

Download Amber MD

2. 安装编译依赖：Installing Amber

yum -y install tcsh make \
               gcc gcc-gfortran gcc-c++ \
               which flex bison patch bc \
               libXt-devel libXext-devel \
               perl perl-ExtUtils-MakeMaker util-linux wget \
               bzip2 bzip2-devel zlib-devel tar

3. 安装Open MPI 4.1.6

wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.bz2
tar -xf openmpi-4.1.6.tar.bz2
./configure --prefix=/opt/openmpi416 --disable-builtin-atomics
make all install -j

vi ~/.bashrc
export PATH=/opt/openmpi416/bin:$PATH
export LD_LIBRARY_PATH=/opt/openmpi416/lib:$LD_LIBRARY_PATH

运行mpiexec -V检查安装是否正确。

4. 安装FFTW库：FFTW Home Page

wget http://www.fftw.org/fftw-3.3.10.tar.gz
tar -xfz fftw-3.3.10.tar.gz
./configure --prefix=/opt/fftw3310 --with-g77-wrappers --enable-shared --enable-threads --enable-openmp --enable-float --enable-sse --enable-sse2 --enable-avx --enable-avx2 --enable-avx512
make -j install

vi ~/.bashrc
export LD_LIBRARY_PATH=/opt/fftw3.3.10/lib:$LD_LIBRARY_PATH

5. 安装Intel OneAPI BaseKit和HPCKit

下载Intel OneAPI BaseKit：Get the Intel® oneAPI Base Toolkit

下载Intel OneAPI HPCKit：Get Intel® oneAPI HPC Toolkit

按照官方教程进行安装。

加载编译环境

# Intel
source /opt/intel/oneapi/setvars.sh --force > /dev/null

export PATH=/opt/intel/oneapi/mpi/2021.15/bin:$PATH
export LD_LIBRARY_PATH=/opt/intel/oneapi/mpi/2021.15/lib:$LD_LIBRARY_PATH

export MKL_HOME=/opt/intel/oneapi/mkl/2025.1
export LD_LIBRARY_PATH=/opt/intel/oneapi/mkl/2025.1/lib:$LD_LIBRARY_PATH

6. 安装Amber和AmberTools

tar xvfj AmberTools24.tar.bz2
tar xvfj Amber24.tar.bz2
cd amber24_src/build
cmake .. -DCMAKE_INSTALL_PREFIX=/opt/Amber24 -DCOMPILER=GNU -DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE -DDOWNLOAD_MINICONDA=TRUE -DUSE_CONDA_LIBS=TRUE -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.4 -DTRUST_SYSTEM_LIBS=TRUE  -DOPENMP=TRUE 2>&1 | tee  cmake.log
make install

vi ~/.bashrc
source /opt/Amber24/amber.sh