centos7 cuda测试_CentOS7配置Amber18/AmberTools18

本文均在CentOS7(release 7.6.1810)版本下进行过的测试
使用gcc4.8.5编译环境。

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。

sudo 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 /mnt/sdd/software/amber/amber18/amber.sh  && source /mnt/sdd/software/amber/amber18/amber.sh
export AMBERHOME=/mnt/sdd/software/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 修复anaconda_libuuid.so.1的错误:

错误:

/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libSM.so: undefined reference to `uuid_unparse_lower@UUID_1.0'

/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libSM.so: undefined reference to `uuid_generate@UUID_1.0'

解决办法：
mv /root/anaconda2/lib/libuuid.so.1 /root/anaconda2/lib/libuuid.so.1_backup
rm -rf /mnt/sdd/software/anaconda2/lib/libuuid.so.1
ln -s /usr/lib64/libuuid.so.1.3.0 /root/anaconda2/lib/libuuid.so.1

4 安装conda环境

conda install --file $AMBERHOME/AmberTools/src/python_requirement.txt

5 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。

「知友」反馈，configure完需要进行source amber.sh

5.1 编译串行版本

cd $AMBERHOME
./configure --with-python /root/anaconda2/bin/python gnu
source /mnt/sdd/software/amber/amber18/amber.sh
make install

# Testing
make test

5.2 编译并行版本

cd $AMBERHOME
./configure --with-python /root/anaconda2/bin/python -mpi gnu
source /mnt/sdd/software/amber/amber18/amber.sh
make install
export DO_PARALLEL="mpirun --allow-run-as-root -np 4 "

./configure --with-python /usr/bin/python -openmp gnu
source /mnt/sdd/software/amber/amber18/amber.sh
make openmp

5.3 编译GPU版本

cd $AMBERHOME
./configure --with-python /root/anaconda2/bin/python -cuda gnu
make install
./configure --with-python /root/anaconda2/bin/python -cuda -mpi gnu
make install

# Testing
make test.cuda
make test.cuda_parallel

6 解决动态库的问题

sudo ldconfig /usr/local/cuda/lib64
sudo ldconfig /mnt/sdd/software/amber/amber18/lib64