GROMACS 安装流程
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 (sobereva.com))
1. 安装 CMake 3.x
- 添加 EPEL 源：
yum install epel-release
- 安装 CMake 3：
yum install cmake3
- 验证 CMake 版本：
cmake3 --version
如果由于某些原因使用 yum 安装失败，或者您没有权限，可从官网手动下载并编译安装。
手动安装
mkdir /share/GROMACS
tar -zxvf cmake-3.29.2.tar.gz -C /share/GROMACS
进入解压后的安装包目录，运行
./bootstrap --prefix=/opt/cmake3 -- -DCMAKE_USE_OPENSSL=OFF
# 这里放在opt目录了
编译
make -j
#可能会爆内存，可以减少核心数比如make -j4 或者去掉-j只用make单线程
make install
路径
echo 'export PATH=/opt/cmake3/bin:$PATH' >> ~/.bashrc
清理
编译前的文件cmake-3.29.2不需要了
[root@mgt opt]# cd /share/GROMACS/
[root@mgt GROMACS]# ls
cmake-3.29.2
[root@mgt GROMACS]# rm -rf cmake-3.29.2/
安装FFTW库
GROMACS 2018依赖于快速傅立叶变换库FFTW 3.3.8
同上解压到某文件夹
如果你的CPU相对较新(cpu-z可以查到，也可以直接搜索)，支持AVX2指令集，可再加上--enable-avx2选项以获得更好性能。
./configure --prefix=/share/fftw338 --enable-sse2 --enable-avx --enable-float --enable-shared --enable-avx2
编译安装
make -j install
安装完成后，fftw库就位于/share/fftw338。同理编译源文件可以删掉了
安装GROMACS
下载解压编译
将文件解压到/share/，cd进入gromacs-2018.8/
[root@mgt gromacs-2018.8]# mkdir build
[root@mgt gromacs-2018.8]# cd build
这里是FFTW338的路径
[root@mgt build]# export CMAKE_PREFIX_PATH=/share/fftw338
如果gcc版本大于等于5，就可以自动检测适配指令集，如果不行，支持AVX2指令集就可以带上-DGMX_SIMD=AVX2_256
cmake .. -DCMAKE_INSTALL_PREFIX=/share/gmx2018.8 -DGMX_SIMD=AVX2_256
如果不是手动编译的cmake或者更新的系统，用cmake3指令 安装
make install -j4
设置环境变量
[root@mgt share]# ls
fftw338 Gaussian gmx2018.8 gromacs-2018.8 home iso slurm20
[root@mgt share]# echo 'source /share/gmx2018.8/bin/GMXRC' >> ~/.bashrc
[root@mgt share]# source ~/.bashrc
检查安装是否成功
[root@mgt share]# gmx -version
:-) GROMACS - gmx, 2018.8 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru
Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl
Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov
Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx, version 2018.8
Executable: /share/gmx2018.8/bin/gmx
Data prefix: /share/gmx2018.8
Working dir: /share
Command line:
gmx -version
GROMACS version: 2018.8
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX2_256
FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: 2024-04-17 02:01:16
Built by: root@mgt [CMAKE]
Build OS/arch: Linux 3.10.0-1160.el7.x86_64 x86_64
Build CPU vendor: Unknown
Build CPU brand: Unknown
Build CPU family: 0 Model: 0 Stepping: 0
Build CPU features: Unknown
C compiler: /usr/bin/cc GNU 4.8.5
C compiler flags: -march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 4.8.5
C++ compiler flags: -march=core-avx2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
gromacs-2018.8安装文件就不需要了，可以删除
[root@mgt share]# ls
fftw338 Gaussian gmx2018.8 gromacs-2018.8 home iso slurm20
