amber安装

安装第一步

(1)把AMBER9.TGZ文件拷贝到 /usr/local/

#cp –rf /mnt/cdrom/AMBER.TGZ /usr/local/

(2)把AMBER9解压到/usr/local/amber9

#tar –zxvf AMBER9.TGZ

(3)设置环境变量

#vi /etc/profile

AMBERHOME=/usr/local/amber9

export AMBERHOME

保存并重启

2．打上bugfix.all补丁到下载

(1)把bugfix.all拷贝到/usr/local/amber9目录下面

#cp –rf bugfix.all /usr/local/amber9

(2) #cd $AMBERHOME

#patch -p0 -N -r patch-rejects < bugfix.all

3．安装INTEL编译器intelforton_9.1.039.tar.gz和intelc++com.tar.gz

#tar –zxvf intelforton_9.1.039.tar.gz;tar –zxvf intelc++com.tar.gz

分别进到解压文件里执行

#./install.sh    ；按说明一步一步安装，默认安装在/opt/intel

4．设置编译器环境

#vi /etc/profile

source /opt/intel/fc/9.1.039/bin/ifortvars.sh

source /opt/intel/cc/9.1.044/bin/iccvars.sh

保存并重启系统

5．进入AMBERHOME/src

#cd $AMBERHOME/src

#./configure ifort_ia32

#make serial

6．测试基本的AMBER

#cd $AMBERHOME/test

#make test.serial

7．安装并行环境，把OPENMPI拷贝到/usr/local目录下

(1)解压出来

 #tar –zxvf openmpi-xxx.tar

(2)设置环境变量

#vi /etc/profile

export FC=/opt/intel/fc/9.1.039/bin/ifort

export CC=/opt/intel/cc/9.1.044/bin/icc

export CXX=/opt/intel/cc/9.1.044/bin/icpc

保存并重启系统

8．安装openmpi，

(1)进入openmpi

#cd /usr/local/openmpi-xxx

#./configure –prefix=/opt/openmpi      ;指定安装路径

#make

#make install

(2) 设置环境变量

#vi /etc/profile

MPI_HOME=/opt/openmpi

export MPI_HOME

PATH=$PATH:$MPI_HOME/bin

export PATH

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPI_HOME/lib

export LD_LIBRARY_PATH

保存并重启系统

9．进入$AMBERHOME/src

(1)   #cd $AMBERHOME/src

(2)   #make clean

(3)   #./configure –openmpi ifort_ia32

(4)   make parallel

10．设置并行环境

(1)vi /etc/profile

#DO_PARALLEL=’mpirun –np 2’

#make test.parallel