安装Ubuntu22.04+nvidia驱动+CUDA-11.7+GRPMACS patch PLUMED

首先是Ubuntu22.4的安装

Ubuntu系统一般直接可以使用RUFUS软件制作U盘启动项，再依照顺序安装Ubuntu系统，这里不赘述。

CUDA-11.7

sudo apt install openssh-server
#如果此命令不成功则先更新一下源
#sudo apt-get update或sudo apt-get upgrade
sudo apt install vim gcc g++ make -y
sudo apt install vim
sudo vim /etc/modprobe.d/blacklist.conf
#在blacklist.conf末尾添加：
#blacklist nouveau
#保存退出
sudo update-initramfs -u

下载NIVIDIA驱动可直接在Ubuntu系统的设置中下载省去编写步骤

验证安装是否成功

nvidia-smi

安装CUDA-11.7

进入cuda-11.7官网

wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-ubuntu2204.pin
sudo mv cuda-ubuntu2204.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget https://developer.download.nvidia.com/compute/cuda/11.7.0/local_installers/cuda-repo-ubuntu2204-11-7-local_11.7.0-515.43.04-1_amd64.deb
sudo dpkg -i cuda-repo-ubuntu2204-11-7-local_11.7.0-515.43.04-1_amd64.deb
sudo cp /var/cuda-repo-ubuntu2204-11-7-local/cuda-*-keyring.gpg /usr/share/keyrings/
sudo apt-get update
sudo apt-get -y install cuda

添加环境变量

sudo vim ~/.bashrc
#在文末添加：
export PATH=/usr/local/cuda-11.7/bin：$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-11.7/bin:$LD_LIBRARY_PATH

保存，退出

source ~/.bashrc
nvcc -V

再者，首先先安装plumed

进入下载好的plumed文件夹

./configure --prefix=/usr/md/plumed  # 编译
make -j
make install -j
vim ~./bashrc     # 添加环境变量
export PATH=/usr/md/plumed/bin：$PATH
export LD_LIBRARY_PATH=/usr/md/plumed/lib:$LD_LIBRARY_PATH
plumed  # 测试
#为了安装对对应版本的gromacs先：
plumed patch -p  # 根据给出的提示安装对应版本的gromacs

安装GROMACS

cd gromacs-2020.6
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON 
-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.7 
# 如果装的是GROMACS >= 2021版，-DGMX_GPU=ON应改为-DGMX_GPU=CUDA
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
# 此处不放心可以再添加一下环境变量试试

测试(如果最后输出ok，则证明带GPU加速的PLUMED的GROMACS安装成功！)

gmx mdrun -h 2> /dev/null | grep -q plumed && echo ok
ok

最后，查看gromacs的版本即可查看：

ren@ren-Precision-7920-Tower:~/gromacs-2022.5/build$ gmx -version
                   :-) GROMACS - gmx, 2022.5-plumed_2.8.2 (-:

Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/ren/gromacs-2022.5/build
Command line:
  gmx -version

GROMACS version:    2022.5-plumed_2.8.2
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support:        CUDA    #拥有GPU加速
SIMD instructions:  AVX2_256
CPU FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library:    cuFFT
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 11.3.0
C compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 11.3.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA compiler:      /usr/local/cuda-11.7/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Tue_May__3_18:49:52_PDT_2022;Cuda compilation tools, release 11.7, V11.7.64;Build cuda_11.7.r11.7/compiler.31294372_0
CUDA compiler flags:-std=c++17;--generate-code=arch=compute_35,code=sm_35;--generate-code=arch=compute_37,code=sm_37;--generate-code=arch=compute_50,code=sm_50;--generate-code=arch=compute_52,code=sm_52;--generate-code=arch=compute_60,code=sm_60;--generate-code=arch=compute_61,code=sm_61;--generate-code=arch=compute_70,code=sm_70;--generate-code=arch=compute_75,code=sm_75;--generate-code=arch=compute_80,code=sm_80;--generate-code=arch=compute_86,code=sm_86;-Wno-deprecated-gpu-targets;--generate-code=arch=compute_53,code=sm_53;--generate-code=arch=compute_80,code=sm_80;-use_fast_math;-D_FORCE_INLINES;-mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA driver:        11.70
CUDA runtime:       11.70