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
参考:
https://blog.csdn.net/u012325865/article/details/73028546
![](https://i-blog.csdnimg.cn/blog_migrate/58674839eb8b7e562848428c62fe1b5c.jpeg)