本记录最近一次使用在2023年2月15日,系统为Deepin 20.8,安装lammps的版本为8 Feb 2023,未发现问题。


本记录最后一次修整在2021年9月24日,系统为Deepin 20.2.3,安装lammps的版本为20 Sep 2021,只适用类似Ubuntu的系统。

安装之前

  1. sudo apt-get install gcc
  2. sudo apt-get install g++
  3. sudo apt-get install gfortran
  4. 可能还有mpi-default-bin, mpi-default-dev,libfftw3-dev, libjpeg-dev and libpng12-dev这些,总之make的时候差什么补什么。具体可以参考/src/MAKE/MACHINES/Makefile.ubuntu里的注释:
# you have to install the packages g++, mpi-default-bin, mpi-default-dev,
# libfftw3-dev, libjpeg-dev and libpng12-dev to compile LAMMPS with this

注1:如果安装过程提示 fatal error: png.h: No such file or directory,则先sudo apt-get install libpng-dev

注2:如果安装过程提示 makeinfo is missing on your system,可以先sudo apt-get install texinfo

准备安装包

查看/src/MAKE/MACHINES/Makefile.ubuntu里的注释,有:

# ubuntu = Ubuntu Linux box, g++, openmpi, FFTW3

因此准备安装包:fftw3、lammps、openmpi(openmpi和mpich2功能相似)

注3:2021年9月24日安装最新的lammps时发现,如果安装之前中提到的项目都安装了,openmpi和fftw3应该不用手动安装,但如果报错的话就还是自己手动安装吧。

注4:通过官网教程上给出的命令从github下载lammps源码出错:

$ git clone -b unstable https://github.com/lammps/lammps.git mylammps
fatal: unable to access 'https://github.com/lammps/lammps.git/': gnutls_handshake() failed: The TLS connection was non-properly terminated.

网上都说是代理的问题,但是我新装的系统根本没有设置什么代理。尝试了下面的取消代理命令:

git config --global --unset http.proxy
git config --global --unset https.proxy

果然没有效果。后来将https改为http就能成功下载了:

git clone -b unstable http://github.com/lammps/lammps.git mylammps

具体原因不知。

安装的时候注意路径

安装:

以下都是用的lammps的默认路径,为了make的时候方便。可以查看\lammps\src\MAKE\OPTIONS 路径下Makefile.fftw 文件和Makefile.g++\_openmpi_link文件里的路径。

  1. (如果直接安装lammps报错就手动安装一下)fftw:(-j4 指调用4核编译)

    sudo ./configure --prefix=/usr/local --enable-float
    sudo make -j4
    sudo make install
  2. (如果直接安装lammps报错就手动安装一下)openmpi:

    sudo ./configure --prefix=/usr/local
    sudo make -j4
    sudo make install
  3. 将/src/MAKE/MACHINES/Makefile.ubuntu复制到/src/MAKE/目录下。在/src目录下:

    sudo make ubuntu -j4

    如果不成功,有时候是library没有立即生效,用

ldconfig

进行更新。

检查安装路径可以用语句:

whereis openmpi

为了简化操作,设置环境变量

在主目录的隐藏文件.bashrc里编辑:

export PATH="$PATH:/home/peachrl/LAMMPS/bin"
export PATH=/usr/local/bin:$PATH

两种写法好像都行。然后,

source ~/.bashrc

让它生效。

看是否成功用语句:

which lmp_ubuntu

运行

运行前移动和改名了:

mv /src/lmp_ubuntu /home/peachrl/LAMMPS/bin/lmp4

运行:(3 指调用3核)

cd /home/peachrl/LAMMPS/lammps-3Mar20/examples/flow
mpirun -np 3 lmp4 < in.flow.couette

附录

Makefile.ubuntu

# ubuntu = Ubuntu Linux box, g++, openmpi, FFTW3

# you have to install the packages g++, mpi-default-bin, mpi-default-dev,
# libfftw3-dev, libjpeg-dev and libpng12-dev to compile LAMMPS with this
# makefile

SHELL = /bin/sh

# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler

CC =        mpic++
CCFLAGS =    -g -O3 # -Wunused
SHFLAGS =    -fPIC
DEPFLAGS =    -M

LINK =        mpic++
LINKFLAGS =    -g -O3
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 -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG

# 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 =
MPI_PATH = 
MPI_LIB =

# FFT library
# see discussion in Section 2.2 (step 6) of manaul
# 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
FFT_PATH = 
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 = -ljpeg -lpng

# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section

include    Makefile.package.settings
include    Makefile.package

EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

# Path to src files

vpath %.cpp ..
vpath %.h ..

# Link target

$(EXE):    $(OBJ) $(EXTRA_LINK_DEPENDS)
    $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
    $(SIZE) $(EXE)

# Library targets

lib:    $(OBJ) $(EXTRA_LINK_DEPENDS)
    $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)

shlib:    $(OBJ) $(EXTRA_LINK_DEPENDS)
    $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
        $(OBJ) $(EXTRA_LIB) $(LIB)

# Compilation rules

%.o:%.cpp $(EXTRA_CPP_DEPENDS)
    $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

%.d:%.cpp $(EXTRA_CPP_DEPENDS)
    $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@

%.o:%.cu $(EXTRA_CPP_DEPENDS)
    $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

# Individual dependencies

depend : fastdep.exe $(SRC)
    @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1

fastdep.exe: ../DEPEND/fastdep.c
    cc -O -o $@ $<

sinclude .depend

Makefile.fftw

FFT_INC =        -DFFT_FFTW3 -I/usr/local/include
FFT_PATH =      -L/usr/local/lib
FFT_LIB =    -lfftw3

Makefile.g++_openmpi_link

MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/local/include
MPI_PATH =     -L/usr/local/lib
MPI_LIB =    -lmpi -lmpi_cxx
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