linux编译lammps (intel mpi) + Voronoi + Colvars package的安装

2021-12-23 By Junwu Chen at IPE, Beijing

随着时间的变更，lammps版本提升、编译器更新等原因，本教程可能不会完全适用

1. 下载lammps最新稳定版源码包（可自行下载需要的版本的源码包:官方;github）

wget方式下载（网络等问题可自行下载后上传服务器）：

wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz --no-check-certificate

解压：

tar -xzf lammps-stable.tar.gz

2. 安装编译lammps

编译环境加载:

1. Intel开发套件(parallel_studio_xe_2018)加载，如我组服务器为：

source /opt/intel/parallel_studio_xe_2018/psxevars.sh

2. 高版本GCC加载(如v_7.5.0，此处采用module方式加载)，因为makefile是由GNU make编写

module load GCC/7.5.0

进入lammps安装目录:

cd lammps-29Sep2021/src/

选择需要安装的package：

1. 选择安装其它的包(如不需要，跳过此步)

如：make yes-kspace yes-manybody yes-molecule

或：make yes-all && make no-lib && make no-ext （！推荐，本教程采用！）

对于老版本： make yes-std && make no-lib

相关命令，详情见官方手册：

make yes-all            # install all packages
make no-all             # uninstall all packages
make yes-basic          # install a few commonly used packages'
make no-basic           # remove a few commonly used packages'
make yes-most           # install most packages w/o libs'
make no-most            # remove most packages w/o libs'
make yes-lib            # install packages that require extra libraries
make no-lib             # uninstall packages that require extra libraries
make yes-ext            # install packages that require external libraries
make no-ext             # uninstall packages that require external libraries

make package-status     # show which packages are currently installed
make ps                 # show which packages are currently installed
make package-installed  # show which packages are currently installed
make pi                 # show which packages are currently installed

注意：有些软件包需要其它库依赖，无法安装，详情见官方手册

Voronoi package的安装
采用官网手册中的Traditional make方法

make lib-voronoi                          # print help message
make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6

注意：下载voro+±0.4.6可能会网络出错导致lib/voronoi/Install.py脚本运行报错，此时自行下载并上传服务器并修改lib/voronoi/Install.py脚本。
voro++下载网站: http://math.lbl.gov/voro++/download/
voro+±0.4.6下载网址: http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz

1. 下载完将安装包上传至lammps-29Sep2021/lib/voronoi目录下
2. 注释Install.py脚本中的79行geturl(url, vorotar)
   
3. 进入lammps-29Sep2021/src/目录

make lib-voronoi args="-b -v voro++0.4.6"
make yes-voronoi

Colvars package的安装
采用官网手册中的Traditional make方法

make lib-colvars args="-m mpi"
make yes-colvars

开始编译(src/目录下)：

make -j 12 intel_cpu_intelmpi

其中的12代表用12核cpu并行编译，若之前编译过或编译失败过，请在正式编译前运行make clean