搭建高性能计算环境（六）、应用软件的安装之lammps

1，上传需要的软件包lammps-stable.tar.gz。

2，解压缩并进入安装目录

tar xvf lammps-stable.tar.gz

cd  lammps-30Oct14

3，如果需要reax、poems等模块，可以进入lib额外添加(标准安装可跳过此步骤)。

cd lib/reax

修改Makefile.ifort文件第31行为： F90FLAGS =      -O3 -xHost -ip -no-prec-div -fPIC

make -f Makefile.ifort

cd ../meam

修改Makefile.ifort文件第30行为： F90FLAGS =      -O3 -xHost -ip -no-prec-div –fPIC

修改Makefile.lammps.ifort文件第4行： meam_SYSLIB = -lifcore -lsvml -liompstubs5 -limf

修改Makefile.lammps.ifort文件第5行： meam_SYSPATH = -L/opt/intel/mkl/lib/intel64/

make -f Makefile.ifort

cd ../poems

修改Makefile.ifort文件第71行为： CCFLAGS =       -O3 -xHost -ip -no-prec-div -fPIC 

make -f Makefile.icc

cd ../../src

make yes-reax

make yes-meam

make yes-poems

也可添加kspace、misc等模块
make yes-kspace
make yes-misc

4，编译fftw2xc

cd /opt/intel/mkl/interfaces/fftw2xc

make libintel64

5，修改src/MAKE/Makefile.mpi

# mpi = default MPI compiler, default MPI



SHELL = /bin/sh



# ---------------------------------------------------------------------

# compiler/linker settings

# specify flags and libraries needed for your compiler



CC =            mpicxx

CCFLAGS = -O3 -xHost -fno-alias -ip -no-prec-div -unroll0

SHFLAGS =       -fPIC

DEPFLAGS =      -M



LINK =          mpicxx

LINKFLAGS =     -O -L/opt/intel/mkl/lib/intel64/

LIB = -lstdc++ -lmkl_core -lmkl_sequential -lmkl_intel_lp64

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 =       

MPI_PATH = 

MPI_LIB =



# 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_MKL -I/opt/intel/mkl/include/fftw

FFT_PATH = 

FFT_LIB =       /opt/intel/mkl/lib/intel64/libfftw2xc_double_intel.a



# 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 =



# ---------------------------------------------------------------------

# 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)



# Path to src files



vpath %.cpp ..

vpath %.h ..



# Link target



$(EXE): $(OBJ)

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

        $(SIZE) $(EXE)



# Library targets



lib:    $(OBJ)

        $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)



shlib:  $(OBJ)

        $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \

        $(OBJ) $(EXTRA_LIB) $(LIB)



# Compilation rules



%.o:%.cpp

        $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<



%.d:%.cpp

        $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@



%.o:%.cu

        $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<



# Individual dependencies



DEPENDS = $(OBJ:.o=.d)

sinclude $(DEPENDS)

6，编译

make mpi -j4

7，设置环境变量，需要重新登陆后生效。

在/etc/profile文件末尾添加如下行：

export PATH=/opt/lammps-30Oct14/src:$PATH

8，测试

 cd /opt/lammps-20Oct14/bench

 mpirun -np 4 lmp_mpi <in.eam

正常运行结束，说明安装成功。

 

lammps下载地址：

http://lammps.sandia.gov/tars/lammps-stable.tar.gz