[转载] 安装 DeepMD-kit v1.0

原作者:曾晋哲

原链接:

https://mp.weixin.qq.com/s/DeQZKwoyxXK7rHhhmdgTmw

https://mp.weixin.qq.com/s/MsEtgnN_mi-auiFyXYUquA

 

 

假定已经安装了Anaconda(建议使用最新版2019.07),已连接互联网,则

1.安装tensorflow(如仅需CPU版本的TensorFlow,则将tensorflow-gpu改为tensorflow):

python -m pip install tensorflow

Successfully installed google-pasta-0.1.7 keras-applications-1.0.8 opt-einsum-3.1.0 tensorboard-2.0.0 tensorflow-estimator-2.0.0 tensorflow-gpu-2.0.0

2.安装deepmd-kit v1.0:

python -m pip install git+https://github.com/deepmodeling/deepmd-kit

Building wheels for collected packages: deepmd-kit
 Building wheel for deepmd-kit (PEP 517) … done
 Created wheel for deepmd-kit: filename=deepmd_kit-1.0.0-cp37-cp37m-linux_x86_64.whl size=268836 sha256=1f5b1149bbf35c0c96c713cc8b607e0626ad0df6451a7
171d4f6b46acc2d4290
 Stored in directory: /tmp/pip-ephem-wheel-cache-zlksq4dl/wheels/a2/80/6c/a26fba79e43199eb4cdba7a3686c5370d3620916f5a0ea23ac
Successfully built deepmd-kit
Installing collected packages: deepmd-kit

Successfully built deepmd-kit
Installing collected packages: deepmd-kit

Successfully installed deepmd-kit-1.0.0

大功告成!现在看一看是否成功安装:

dp -h

usage: dp [-h] {train,freeze,test} …
DeePMD-kit: A deep learning package for many-body potential energy
representation and molecular dynamics
optional arguments:
 -h, –help           show this help message and exit
Valid subcommands:
 {train,freeze,test}
   train              train a model
   freeze             freeze the model
   test               test the model

现在,DeePMD-kit v1.0.0已成功安装。下一期将介绍如何用DP编译LAMMPS

 

TensorFlow 安装

最新版本的 TensorFlow 要求 GLIBC 2.17 以上,尽管推荐做法是找一台最新系统的机子,但是有时候系统的类型不是由自己决定的,通常又没有root权限,又想在所有机子上都能运行 TensorFlow 。

刚好手里有一个超算账号,系统是 Red Hat 4.4.7 ,GLIBC 版本是 2.12 ,就以此为例,安装CPU版本的TensorFlow(反正没有权限也安装不了GPU版本需要的驱动)。


一、用 Anaconda 3 安装 TensorFlow 1.8

1.安装 Anaconda 3

Linux软件安装②|Anaconda3

2.创建 TensorFlow 环境

conda create -n tensorflow pip python=3.6
#Proceed ([y]/n)? 输y
source activate tensorflow #激活环境
pip install tensorflow -i https://pypi.tuna.tsinghua.edu.cn/simple/
#这两天由于众所周知的原因,Google官方的镜像又下载不了了,所以这里用了清华大学的镜像

二、安装 gcc

这时候打开 Python ,执行 import tensorflow ,提示:

ImportError: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.7′ not found

conda install -c psi4 gcc-5 
#Proceed ([y]/n)? 输y
LD_LIBRARY_PATH=$HOME/anaconda3/envs/tensorflow/lib:$LD_LIBRARY_PATH

再此运行 Python,不再提示这个问题。

三、安装 GLIBC 2.21

但是提示:

ImportError: /lib64/libc.so.6: version `GLIBC_2.16′ not found

本来应该安装GLIBC 2.17,但是我发现从2.16到2.19都有个bug,不能运行Python 3.6。于是我们安装GLIBC 2.21。

1.下载GLIBC 2.21并编译GLIBC 2.21

wget http://mirror.rit.edu/gnu/libc/glibc-2.21.tar.gz
tar zxvf glibc-2.21.tar.gz
mkdir glibc-2.21-build glibc-2.21-install
cd glibc-2.21-build
../glibc-2.21/configure --prefix=`readlink -f ../glibc-2.21-install` 
make && make install

然后就报错了:

checking version of as… 2.20.51.0.2, bad
checking version of ld… 2.20.51.0.2, bad
These critical programs are missing or too old: as ld

仔细看看INSTALL文件,要求GNU ‘binutils’ 2.22 or later,但系统只装了2.20。

2.下载并编译binutils 2.30

wget ftp://ftp.gnu.org/gnu/binutils/binutils-2.30.tar.gz
tar zxvf binutils-2.30.tar.gz
cd binutils-2.30
./configure --prefix=`readlink -f ../binutils-2.30-install` 
make && make install
#加入环境变量
PATH=$HOME/software/binutils-2.30-install/bin:$PATH

3.重新编译glibc 2.21

cd glibc-2.21-build
../glibc-2.21/configure --prefix=`readlink -f ../glibc-2.21-install` 
make && make install

Warning: ignoring configuration file that cannot be opened: … /software/glibc-2.21-install/etc/ld.so.conf: No such file or directory

将/etc 目录的ld.so.conf复制到指定目录后重新安装:

cp /etc/ld.so.conf ../glibc-2.21-install/etc/
make install

安装成功。

四、运行TensorFlow

source activate tensorflow
$HOME/software/glibc-2.21-install/lib/ld-2.21.so --library-path $HOME/anaconda3/envs/tensorflow/lib:$HOME/software/glibc-2.21-install/lib:/lib64:$LD_LIBRARY_PATH `which python`

在Python内输入:

# Python
import tensorflow as tf
hello = tf.constant('Hello, TensorFlow!')
sess = tf.Session()
print(sess.run(hello))

b’Hello, TensorFlow!’

运行成功。我们可以运行的命令记录在.bashrc中:

echo 'alias tf='"'"'$HOME/software/glibc-2.21-install/lib/ld-2.21.so --library-path $HOME/anaconda3/envs/tensorflow/lib:$HOME/software/glib-2.21-install/lib:/lib64:$LD_LIBRARY_PATH `which python`'"'">>$HOME/.bashrcsource $HOME/.bashrc

即可用 tf 代替装了 TensorFlow 的 Python。