CentOS7.6 安装配置Amber18/AmberTools18（GPU加速版）

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

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参考：

https://blog.csdn.net/u012325865/article/details/73028546

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