windows7 下安装 lammps :
几乎就不用安装,只是要注意一点的是mpich2的 smpd
win7中管理员运行cmd.exe 进入安装目录下的bin文件夹 运行smpd -install
手动注册一下 smpd.exe -regserver
注册用户:mpiexec -register (使用当前使用的账户名称)
用 mpiexec -validate 检验是否 成功
PS: 在桌面以管理员权限 打开msys的快捷方式。在/usr/bin 下 建一个使用 mpi 的脚本lmpmpi:
#!/bin/bash
mpiexec.exe -n 2 lmp_win_mpi.exe -in $1
Suse server11 上的安装:
因为服务器上已将安装openmpi了,lammps的平行就使用它,fftw 使用3.3.2 还是遇到问题,暂时放弃 返回使用2.1.5
使用g++编译,编译过程中提示openmpi找不到一些文件的 变量定义。估计是版本 和库 的问题。
接着找到以下参考,证明fftw 使用3.3.2 还是可以使用的
参考:http://hi.baidu.com/kongkongjian1/item/b0d62d4c5b0a7d0d6cc2f0eb
1安装好vmware 8 SLES 11 SP2 INTEL 编译器 openmpi
2 安装fftw 3.3.1
解压后
./configure –prefix=/opt/fftw #路径可以不给出
make
sudo make install
3 修改src/Make/Makefile.openmpi
去掉编译参数 "-W"
替换三行
替换内容如下
############################
FFT_INC = -I/opt/fftw/include -DFFT_FFTW3
FFT_PATH = -L/opt/fftw/lib
FFT_LIB =/opt/fftw/lib/libfftw3.a # -lfftw
############################
4 make yes-all
make no-gpu no-kim no-user-cuda no-user-atc no-user-awpmd
5 把lib下面meam和reax文件夹下的Makefile.lammps 中的-lompstub改成-liompstubs5
6 用ifort 或者icc命令make lib下文件夹中的meam poems reax
命令如make -f Makefile.ifort
7cd src
make openmpi
编译完成为src文件夹下的lmp_openmpi(12MB)。没有安装GPU CUDA KIM USER-ATC USER-AWPMD.
####
最终使用openmpi修改为
###########################################################################
# openmpi = Fedora Core 6, mpic++, OpenMPI-1.1, FFTW2
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpic++
CCFLAGS = -O2 \
-funroll-loops -fstrict-aliasing -Wall -Wno-uninitialized #去掉了 -W参数
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpic++
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rcsv
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
# 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/public/software/mpi/openmpi1.3.4-intel/include
MPI_PATH = -L/public/software/mpi/openmpi1.3.4-intel/lib
MPI_LIB = -lpthread -lmpi
# 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/opt/fftw-3.3.2/include -DFFT_FFTW3
FFT_PATH = -L/opt/fftw-3.3.2/lib
FFT_LIB = /opt/fftw-3.3.2/lib/libfftw3.a #-lfftw
# 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/public/software/lmp/jpeg/include
#JPG_PATH = -L/public/software/lmp/jpeg/lib
#JPG_LIB = /public/software/lmp/jpeg/lib/libjpeg.so.8
# ---------------------------------------------------------------------
# build rules and dependencies
# no need to 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)
# 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) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
sinclude $(DEPENDS)
########################################################################################
编译好了 jpeg 可是如果不屏蔽,编译完的lmp_openmpi 运行时提示找不到 jpeg的库
cp lmp_openmpi 到usr/bin 下 修改权限 chmod 755 lmp_openmpi
测试通过 mpirun -4 lmp_openmpi < in.example
测试lmp并行计算
$ sudo mv ~/lammps/src/lmp_g++ /usr/bin $ mkdir ~/md $ cp ~/lammps/examples/colloid/in.colloid ~/md $ cd ~/md $ /usr/local/mpich2/bin/mpirun -n 2 lmp_g++ < in.colloid |
再次安装还是出了点问题:
看了下别人的总结http://blog.csdn.net/shixha/article/details/10648171
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
不小心一开始没有该对
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