硬件环境：
1. 解压安装包
tar jxvf AmberTools18.tar.bz2 tar jxvf Amber18.tar.bz2
2. 安装环境依赖
需要使用默认的CentOS7编译器，以及gcc4.8.5编译的CUDA组件。
su root yum install gcc gcc-gfortran gcc-c++ flex tcsh zlib-devel \ bzip2-devel libXt-devel libXext-devel libXdmcp-devel \ tkinter openmpi openmpi-devel perl perl-ExtUtils-MakeMaker \ patch bison boost-devel #~/.bashrc中添加环境 #AMBER test -f /opt/amber/amber18/amber.sh && source /opt/amber/amber18/amber.sh export AMBERHOME=/opt/amber/amber18 export CUDA_HOME=/usr/local/cuda export PATH=$PATH:$CUDA_HOME/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib64
3. 安装conda环境
conda install --file $AMBERHOME/AmberTools/src/python_requirement.txt
4. 编译AMBER:
先安装串行，再安装并行，最后加入gpu。
第一次进行configure的时候会检查补丁，推荐安装补丁。
5.1 编译串行版本
cd $AMBERHOME ./configure --with-python /root/anaconda3/bin/python gnu make install # Testing make test
5.2 编译并行版本
cd $AMBERHOME ./configure --with-python /root/anaconda3/bin/python -mpi gnu make install export DO_PARALLEL="mpirun --allow-run-as-root -np 4 " ./configure --with-python /usr/bin/python -openmp gnu make openmp
5.3 编译GPU版本
cd $AMBERHOME ./configure --with-python /root/anaconda3/bin/python -cuda gnu make install ./configure --with-python /root/anaconda3/bin/python -cuda -mpi gnu make install # Testing make test.cuda make test.cuda_parallel
