LAMMPS安装教程
Tips:安装过程不难,细心仔细,遇到问题百度会帮你
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打开CentOS系统,进入root用户。
一.32位库环境配置
在所有安装开始之前,先配置好所涉及的32位库文件。具体过程如下:
分别使用以下命令,将所查找到的所有文件,使用yum install 文件名更新或安装,gcc安装gcc、gcc-c++、gcc-gortran。
yum list libstdc*
yum list glibc*
yum list libgcc*
yum list gcc*
Xorg X11 libXss runtime library
yum install libXScrnSaver
yum install libXScrnSaver.i686
更新、安装好后再输入这三个命令查看是否已经安装完毕,特别注意以.i686为后缀的文件一定要安装好,那就是32位库文件。
安装好后检查一下,例如,使用 yum list libstdc*命令检查可见,所有安装包都可在Installed Packages一栏中找到。
切换成普通用户继续之后的操作
二. mpich 3.2.1 的安装
openmpi-3.1.3版gcc编译器有intel库无法连接,lammps运行会出现错误,影响运行,据说高版本已经修复该问题
(1)程序安装
逐步输入以下命令:
tar zxvf mpich-3.2.1.tar.gz
cd mpich-3.2.1
./configure --prefix=/home/gg/mpich-3.2.1
make
make install
注意:/home/gg/mpich-3.2.1为安装目录,可自行替换。
(2)环境变量设置
配置环境变量:
vim ~/.bashrc
在~/.bashrc中加入以下语句:
# mpich 3.2.1 environment variable
export MPI=/home/gg/mpich-3.2.1
export PATH=$MPI/bin:$PATH
export LD_LIBRARY_PATH=$MPI/lib:$LD_LIBRARY_PATH
export MANPATH=$MANPATH:$MPI/share/man
export INFOPATH=$INFOPATH:$MPI/share/man
export INCLUDE=$MPI/include:$INCLUDE
(3)测试安装成功
1.输入which mpirun mpif90 检查环境变量是否设置成功,检查环境变量是否设置成功,成功则显示路径。
2.在mpich-3.2.1安装包路径中(注意是安装包路径!!),输入以下命令:
cd examples/
make
mpicc hello_c.c –o hello_c
mpirun -np 4 ./hello_c
出现以下界面则安装成功。
三. fftw 3.3.9的安装
(1)程序安装
逐步输入以下命令:
tar zxvf fftw-3.3.9.tar.gz
cd fftw-3.3.9/
./configure --prefix=/home/gg/fftw-3.3.9 --enable-mpi
make
make install
注意: /home/gg/fftw-3.3.9 为安装目录,可自行替换。
(2)环境变量设置
方法同上,更改bashrc文件
vim ~/.bashrc
在文件中加入以下语句:
# fftw 3.3.9 environment variable
export PATH=/home/gg/fftw-3.3.9/bin:$PATH
export LD_LIBRARY_PATH=/home/gg/fftw-3.3.9/lib:$LD_LIBRARY_PATH
注意:安装路径如有不同请自行替换。
最后更新环境变量:
source ~ /.bashrc
(3)测试安装成功
检查 “/home/gg/fftw-3.3.9/lib/libfftw3_mpi.a”文件是否存在,若存在,则安装成功。
四. Lammps安装
(1)准备工作
将Lammps拷贝到工作站中
(2)安装
1.解压包:
tar zxvf lammps-xxx.tar
2.修改makefile:
cd /home/gg/software/lammps-11Jan12/src/MAKE/
vim Makefile.mpi
修改以下红色标记,将路径修改为自己的安装路径:
# mpi = MPI with its default compiler SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # specify flags and libraries needed for your compiler CC = mpicxx CCFLAGS = -g -O3 SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpicxx LINKFLAGS = -g -O LIB = SIZE = size ARCHIVE = ar ARFLAGS = -rc SHLIBFLAGS = -shared # --------------------------------------------------------------------- # LAMMPS-specific settings, all OPTIONAL # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings # see possible settings in Section 2.2 (step 4) of manual LMP_INC = -DLAMMPS_GZIP # MPI library # see discussion in Section 2.2 (step 5) of manual # MPI wrapper compiler/linker can provide this info # can point to dummy MPI library in src/STUBS as in Makefile.serial # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/home/gg/mpich-3.5.0/include MPI_PATH = -L/home/gg/mpich-3.5.0/lib MPI_LIB = -lmpi # FFT library # see discussion in Section 2.2 (step 6) of manual # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW3 -I/home/gg/fftw-3.3.9/include FFT_PATH = -L/home/gg/fftw-3.3.9/lib FFT_LIB = -lfftw3 # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual # only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC # INC = path(s) for jpeglib.h and/or png.h # PATH = path(s) for JPEG library and/or PNG library # LIB = name(s) of JPEG library and/or PNG library JPG_INC = JPG_PATH = JPG_LIB = ............... |
注意:黄色部分为自己安装路径
保存退出
3.编译package
(1)编译标准库
输入下述命令:
cd ~/software/lammps-11Jan12/src
make yes-ASPHERE yes-BODY yes-CLASS2 yes-COLLOID yes-COMPRESS yes-CORESHELL yes-DIPOLE yes-GRANULAR yes-KSPACE yes-MANYBODY yes-MC yes-MISC yes-MOLECULE yes-MPIIO yes-OPT yes-PERI yes-QEQ yes-REPLICA yes-RIGID yes-SHOCK yes-SNAP yes-SPIN yes-SRD
(2)编译poems
#参见lammps用户手册4.1 Standard Packages
cd ~/software/lammps-11Jan12/lib/poems
rm *.o
make -f Makefile.g++
cd ~/software/lammps-11Jan12/src
make yes-poems
(3)编译meam
#参见lammps用户手册4.1 Standard Packages
更改Makefile文件:
cd ~/software/lammps-11Jan12/lib/meam
rm *.o
make -f Makefile.gfortran
cp Makefile.lammps.gfortran Makefile.lammps
cd ~/software/lammps-11Jan12/src
make yes-meam
(4)编译reax
#参见lammps用户手册4.1 Standard Packages
更改Makefile文件:
cd ~/software/lammps-11Jan12/lib/reax
rm *.o
make -f Makefile.gfortran
cp Makefile.lammps.gfortran Makefile.lammps
cd ~/software/lammps-11Jan12/src
make yes-reax
(5)编译user库
cd ~/software/lammps-11Jan12/src
make yes-USER-BOCS yes-USER-CGDNA yes-USER-CGSDK yes-USER-DIFFRACTION yes-USER-DPD yes-USER-DRUDE yes-USER-EFF yes-USER-FEP yes-USER-INTEL yes-USER-LB yes-USER-MANIFOLD yes-USER-MEAMC yes-USER-MESO yes-USER-MGPT yes-USER-MISC yes-USER-MOFFF yes-USER-MOLFILE yes-USER-OMP yes-USER-PHONON yes-USER-PTM yes-USER-QTB yes-USER-REAXC yes-USER-SMTBQ yes-USER-SDPD yes-USER-SPH yes-USER-TALLY yes-USER-UEF
4.编译Lammps
输入make mpi开始安装编译Lammps
如果编译成功,会生成一个lmp_mpi文件。
5.导入PATH
编辑在bashrc文件:
vi ~/.bashrc
在文件最末端,输入以下内容:
export PATH=/home/guoxin/software/lammps-11Jan12/src:$PATH
更新配置文件
source ~/.bashrc
7.测试
进入lammps自带例子文件夹下
cd /home/gg/software/lammps-11Jan12/examples/shear
mpirun -np 3 lmp_mpi < in.shear
若之前没更改环境文件,应加上绝对路径
/home/gg/mpich-3.5.30bin/mpirun -np 3 /home/gg/.../in.shear
/home/gg/mpich-3.5.0/bin/mpirun为mpich安装路径下的mpirun位置
-np 3为调用3个cpu核数
/home/gg/.../in.shear为in.shear文件的位置