LAMMPS安装总结

硬件: SMP服务器, 4个CPU(XeonE7450), 内存64G,ATI显卡

软件:Red Hat Enterprise 4, gcc3.4.6

前言: 由于服务器比较老,而且我没有root权限,安装起来很不方便,各种软件和库都没有,都是下载后手工编译安装的,用了3天时间,除了GPU和CUDA因为是ATI显卡的原因无法安装外,成功安装了各个包

Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package DIPOLE
Installed YES: package FLD
Installed  NO: package GPU
Installed YES: package GRANULAR
Installed YES: package KIM
Installed YES: package KSPACE
Installed YES: package MANYBODY
Installed YES: package MC
Installed YES: package MEAM
Installed YES: package MISC
Installed YES: package MOLECULE
Installed YES: package OPT
Installed YES: package PERI
Installed YES: package POEMS
Installed YES: package REAX
Installed YES: package REPLICA
Installed YES: package RIGID
Installed YES: package SHOCK
Installed YES: package SRD
Installed YES: package VORONOI
Installed YES: package XTC


Installed YES: package USER-ATC
Installed YES: package USER-AWPMD
Installed YES: package USER-CG-CMM
Installed YES: package USER-COLVARS
Installed  NO: package USER-CUDA
Installed YES: package USER-EFF
Installed YES: package USER-MISC
Installed YES: package USER-OMP
Installed YES: package USER-MOLFILE
Installed YES: package USER-PHONON
Installed YES: package USER-REAXC
Installed YES: package USER-SPH

参考网上教程和manul安装还比较顺利,但是有几个包特别麻烦...写出来分享下,希望能帮到需要的人

USER-ATC:  先将MPI的头文件,用-I包含,但由于gcc版本太低,所以总是报错,手动安装gcc4.8.1后libatc.a顺利编译, 但lammps编译时报错dsygvd,dgesvd两个函数找不到,google下发现是BLAS和LAPACK里的函数,由此怀疑是lammps自带的linalg库有问题,自己下载GotoBLAS或者LAPACk都可以,解决

USER-AWPMD: 这个也比较坑爹,主要是makefile只有Makefile.openmpi,但是我编译lammps用的mpich,文档又说库和lammps编译时用的mpi要一致,解决办法是手动修改Makefile.openmpi中CC编译器为mpich的mpicxx,这样有一些警告,但是能顺利编译库,和lammps

USER-REAXC: 要将连接库的名字与ifort库中的完全一致,-lifcore -lsvml -liompstubs5 -limf, 特别是-liompstubs5跟以前的版本不一样了

KIM: 这个很好解决,下载openkim-ati库,google下即可,下载编译后将头文件的目录-I连接上

VORONOI:  也需要自己下载voro++源码,手动编译出来即可

libjpeg: 下载libjpeg源码,手工编译即可

附上我lammps的makefile,仅供参考

# my = RedHat Linux box, g++ (v3), MPICH, FFTW3

SHELL = /bin/sh

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

CC =        g++481 //自己link的gcc4.8.1
CCFLAGS =   -g -O
SHFLAGS =   -fPIC
DEPFLAGS =  -M

LINK =      g++481 //同上
LINKFLAGS = -g -O
LIB =
SIZE =      size

ARCHIVE =   ar
ARFLAGS =   -rc
SHLIBFLAGS =    -shared

# ---------------------------------------------------------------------
# LAMMPS-specific settings
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"

# LAMMPS ifdef settings, OPTIONAL
# see possible settings in doc/Section_start.html#2_2 (step 4)

LMP_INC =   -DLAMMPS_GZIP -DLAMMPS_JPEG //jpeg包

# MPI library, REQUIRED
# see discussion in doc/Section_start.html#2_2 (step 5)
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library

MPI_INC = -I/home/xhshi/mpich/include/ -DMPICH_SKIP_MPICXX //mpich头文件
MPI_PATH =-L/home/xhshi/mpich/lib //mpich库
MPI_LIB = -lmpich -lpthread -lmpl //库名称,要一致

# FFT library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 6)
# 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 =  -I/home/xhshi/fftw3/include -DFFT_FFTW3  //fftw3.3.2版本
FFT_PATH = -L/home/xhshi/fftw3/lib
FFT_LIB =   -lfftw3

# JPEG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# only needed if -DLAMMPS_JPEG listed with LMP_INC
# INC = path for jpeglib.h
# PATH = path for JPEG library
# LIB = name of JPEG library

JPG_INC = -I/home/xhshi/jpeg6b/include
JPG_PATH =  -L/home/xhshi/jpeg6b/lib
JPG_LIB =   -ljpeg

我的总结:

1.如果编译出现,XXX库找不到, 那么很有可能-L 没有连接对

2. 如果编译出现,XXX.h找不到, 那么很有可能-I 没有连接好

3. 如果出现结构体没有定义, 那么很有可能编译器版本太低

4. 如果出现函数找不到,那么很有可能静态库.a中没有该.o目标文件,应该ar或nm命令查看.a库

5.如果发现问题,首先思考分析下原因,接着在google