一。安装VMD 原帖地址http://www./thread-13305-1-1.html 安装前需先安装两个软件包 $sudo apt-get install csh $sudo apt-get install libstdc++5 下载vmd-1.8.7.bin.LINUX.opengl.tar.gz 下载地址:http://www.ks./Development/Download/download.cgi $tar xvzf vmd-1.8.7.bin.LINUX.opengl.tar.gz $cd vmd-1.8.7 $./configure $cd src $sudo make install (提示 "VMD installation complete. Enjoy!" ) $vmd 出现vmd界面,安装成功。 不同机器需要不同版本,之前下载vmd-1.8.7.bin.LINUXAMD64.opengl.tar.gz,虽然也能安装成功,但是最后输入vmd后会显示找不到vmd_linux命令。 二、安装ssh通信 $sudo vim /etc/hosts 修改此文件如下: 127.0.0.1 localhost 127.0.1.1 lm-desktop 192.168.76.43 lm-desktop 此时可以使用ssh lm-desktop测试ssh通信是否正常。 注:lm-desktop 是你的主机名 安装设置ssh sudoapt-get install openssh-clientopenssh-server 以设定的用于启动mpi计算的用户登录,运行 ssh-keygen-t rsa #对于所有提示直接回车即可 这将生成一个密钥对,分别存放在~/.ssh/id_rsa和~/.ssh/id_rsa.pub文件内。 然后进行访问授权,运行: cp ~/.ssh/id_rsa.pub ~/.ssh/authorized_keys chmod go-rwx~/.ssh/authorized_keys ssh-agent $SHELL ssh-add 以上配置ssh完毕。 三、编译安装lammps 安装前首先要安装fftw,mpich 1.安装fftw 下载fftw-2.1.5.tar.gz 下载地址:http://www./download.html $tar xvzf fftw-2.1.5.tar.gz $cd fftw-2.1.5 $sudo ./configure --prefix=/opt/mathlib/fftw215-gnu –enable-float $sudo make $sudo make install 2.安装mpich 下载mpich.tar.gz下载地址:http://www./gb/learn/learn1/200604110001.html $tar xvzf mpich.tar.gz $cd mpich-1.2.7p1/ $./configure--prefix=/opt/mpich-gnu -rsh=ssh $sudo make $sudo make install 3.安装lammps 下载地址:http://lammps./download.html 要切换到根用户 $sudo -i $tar xvzf lammps-upgrade.tar.gz $cd lammps-28Oct08/ $cd src $gedit MAKE/Makefile.linux 修改mpich和fftw的安装路径.把里面的内容替换为如下内容 # linux = RedHat Linux box, Intel icc, MPICH2, FFTW SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # specify flags and libraries needed for your compiler CC = icc CCFLAGS = -O -DLAMMPS_GZIP -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK -I/opt/mathlib/fftw215-gnu/include -I/opt/mpich-gnu/include DEPFLAGS = -M LINK = icc LINKFLAGS = -O LIB = -lstdc++ ARCHIVE = ar ARFLAGS = -rc SIZE = size # --------------------------------------------------------------------- # LAMMPS-specific settings # specify settings for LAMMPS features you will use # LAMMPS ifdef options, see doc/Section_start.html LMP_INC = -DLAMMPS_GZIP # MPI library, can be src/STUBS dummy lib # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -DMPICH_IGNORE_CXX_SEEK MPI_PATH = -L/opt/mpich-gnu/lib MPI_LIB = -lmpich -lpthread # FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package # INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW FFT_PATH = -L/opt/mathlib/fftw215-gnu/lib FFT_LIB = -lfftw # additional system libraries needed by LAMMPS package libraries # these settings are IGNORED if the corresponding LAMMPS package # (e.g. gpu, meam) is NOT included in the LAMMPS build # SYSLIB = names of libraries # SYSPATH = paths of libraries gpu_SYSLIB = -lcudart meam_SYSLIB = -lifcore -lsvml -lompstub -limf reax_SYSLIB = -lifcore -lsvml -lompstub -limf user-atc_SYSLIB = -lblas -llapack -latc gpu_SYSPATH = -L/usr/local/cuda/lib64 meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib user-atc_SYSPATH = -L/home/wlfhg/lammps-30Mar10/lib/atc # --------------------------------------------------------------------- # build rules and dependencies # no need to edit this section include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB) # Link target $(EXE): $(OBJ) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library target lib: $(OBJ) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) # Compilation rules %.o:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ # Individual dependencies DEPENDS = $(OBJ:.o=.d) include $(DEPENDS) 保存后退出 $make linux 4.编译xmovie小工具 原帖地址http://www./viewthread.php?tid=8265&highlight=xmovie xmovie是lammps附带的一个小工具,可以很方便的查看dump文件。在RedHat下,xmovie直接make就可以通过,但在ubuntu下编译还需要先安装一些额外的包。 打开“系统”=>“系统管理”=>“新立得软件包管理器” 在“新立得”中,以“libx”为关键词,搜索并安装以下各包: libxaw7 libxaw7-dev libxt6 libxt6-dev 进入到“xmovie”所在目录,执行如下命令:make 在“xmovie”文件夹中会产生一个名为“xmovie”的可执行文件。 四、安装fortran 安装前需要先安装其他程序 $sudo apt-get install build-essential $sudo apt-get install libstdc++5 下载非商业版fortran包l_cprof_p_11.1.064_ia32.tgz 下载地址:https://registrationcenter.intel.com/RegCenter/AutoGen.aspx?ProductID=1322&AccountID=&EmailID=&ProgramID=&RequestDt=&rm=NCOM?= 下载需要输入你的邮箱,然后会给你的邮箱发个序列号和licence $tar xvzf l_cprof_p_11.1.064_ia32.tgz $cd l_cprof_p_11.1.064_ia32 $sudo /.install.sh 然后根据默认选择,输入序列号,最后accept,安装成功。 验证安装,可以执行命令$ifort-v 提示ifortcommand cann't found,不急。打开主文件夹下.bashrc文件,在最后加入一行命令source/opt/intel/Compiler/11.1/064/bin/ifortvars.sh ia32 ,保存退出,再执行命令$ifort-v 一切ok。 |
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