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amber12 GNUintel 编译安装?? 2012-12-18 22:26:07|??分类：?默认分类|举报|字号?订阅 一、amber12 gnu编译安装方法：1. 换源：cd /etc/aptsed /universe$/ s/^.// sources.list /tmp/sources.listsudo mv sources.list sources.list.backupsudo mv /tmp/sources.list sources.listcd ~sudo apt-get update2. 安装必要程序：sudo apt-get install gcc g++ libxt-dev libxext-dev flex gfortran tcsh libnetcdf-dev patch csh bison xorg-dev zlib1g-dev libbz2-devmpi我们选择安装openmpi-dev,即sudo apt-get install openmpi-dev openmpi-bin3. 解压ambertools12和amber12：cd /home/zheng/softwares/ambertar xfj AmberTools12.tar.bz2tar xfj Amber12.tar.bz24. 设置环境变量：cd amber12echo export AMBERHOME=$PWD ~/.bashrcecho export PATH=$PATH:$AMBERHOME/bin ~/.bashrcecho export DO_PARALLEL=mpirun -np 24 ~/.bashrc （N是核心数。source这一步如果出错的话，可以将其删除）source ~/.bashrc注：source之后用emacs ~/.bashrc打开检查一下，如果有问题手动修改。5. 打补丁：$AMBERHOME/patch_amber.py --update-tree6. 安装串行版amber12：./configure gnumake installmake test7. 安装并行版amber12：make clean./configure -mpi gnumake installexport DO_PARALLEL=mpirun -np 2make test二、amber12 intel编译安装：1. 安装intel编译器（intel官网下载）。我装的版本是l_ccompxe_intel64_2011.9.293，l_fcompxe_intel64_2011.9.293，l_mkl_56_intel64，l_mpi_p_08。安装方法google一下，比较简单，直接./install.sh，按照提示一步一步来就可以了。安装完成之后，要在emacs ～/.bashrc中添加如下：source /opt/intel/composer_xe_2011_sp1.9.293/bin/iccvars.sh intel64source /opt/intel/composer_xe_2011_sp1.9.293/bin/ifortvars.sh intel64source /opt/intel/composer_xe_2011_sp1.9.293/mkl/bin/intel64/mklvars_intel64.shsource /opt/intel/impi/08/bin64/mpivars.sh?保存。然后source ~/.bashrc。终端中输入which icc和which ifort，输出的路径正确算是安装成功。2.sudo apt-get install gcc g++ libxt-dev libxext-dev flex gfortran tcsh libnetcdf-dev patch csh bison xorg-dev zlib1g-dev libbz2-dev3.解压ambertools12和amber12：cd /home/zheng/softwares/ambertar xfj AmberTools12.tar.bz2tar xfj Amber12.tar.bz24. 设置环境变量：emacs ~/.bashrcexport AMBERHOME=/home/zheng/softwares/amber/amber12export MKL_HOME=/opt/intel/composer_xe_2011_sp1.9.293/mklexport MPI_HOME=/opt/i