LAMMPS 即 Large-scale Atomic/Molecular Massively Parallel Simulator，大规模原子分子并行模拟器，主要用于分子动力学相关的一些计算和模拟工作。
系统: Centos7.6 x86_64
编译器：GCC-9.3
1、安装OpenMPI
# yum install -y gcc gcc-c++ gcc-gfortran # wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.4.tar.bz2 # tar jxvf openmpi-4.0.4.tar.bz2 # cd openmpi-4.0.4 # mkdir build && cd build # ../configure --prefix=/usr/local/openmpi-4.0.4 CC=gcc CXX=g++ FC=gfortran F77=gfortran # make -j # make install
配置OpenMPI环境变量
# vim ~/.bashrc export PATH=/usr/local/openmpi-4.0.4/bin:$PATH export LD_LIBRARY_PATH=/usr/local/openmpi-4.0.4/lib:$LD_LIBRARY_PATH export MANPATH=/usr/local/openmpi-4.0.4/share/man:$MANPATH
2、安装FFTW
# wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.8.tar.gz # tar zxvf fftw-3.3.8.tar.gz # cd fftw-3.3.8 # mkdir build && cd build # ../configure --prefix=/usr/local/fftw --enable-mpi --enable-openmp --enable-shared --enable-static # make -j # make install # vim ~/.bashrc export PATH=/usr/local/fftw/bin:$PATH export LD_LIBRARY_PATH=/usr/local/fftw/lib:$LD_LIBRARY_PATH
3、安装LAMMPS
# yum install libjpeg-devel libpng-devel # wget https://lammps.sandia.gov/tars/lammps-3Mar20.tar.gz # wget https://github.com/lammps/lammps/archive/stable_3Mar2020.tar.gz # tar zxvf lammps-3Mar20.tar.gz # cd lammps-3Mar20/src # vim MAKE/Makefile.mpi
配置MPI路径
CC = mpicxx CCFLAGS = -g -O3 -fopenmp SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpicxx LINKFLAGS = -g -O3 -fopenmp MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 MPI_PATH = MPI_LIB = LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 #LMP_INC = or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL FFT_INC = -DFFT_FFTW3 -I/usr/local/fftw/include FFT_PATH = -L/usr/local/fftw/lib FFT_LIB = -lfftw3
安装模块
# make yes-MANYBODY
编译LAMMPS
# make -j mpi # mkdir -p /usr/local/lammps/bin # cp lmp_mpi /usr/local/lammps/bin/ # vim ~/.bash.rc export PATH=/usr/local/lammps/bin:$PATH export LD_LIBRARY_PATH=/usr/local/lammps/lib:$LD_LIBRARY_PATH
4、并行测试案例
# cd ../examples/shear # mpirun --allow-run-as-root -np 8 --hostfile hostlist lmp_mpi < in.shear