查看系统版本:
1.docker(docker ce)安装(是否运行在容器中取决于自己)
下载:https://www.docker.com/products/docker-engine
安装:https://docs.docker.com/install/linux/docker-ce/ubuntu/
2.Installing Ubuntu(18.04) requirements(若使用docker,去掉sudo)
$ sudo apt-get update
$ sudo apt install -y --no-install-recommends \
ca-certificates curl g++ git libmysqlclient-dev ocl-icd-opencl-dev \
pkg-config python python-dev python3.6 python3.6-dev python3-distutils \
unzip zip zlib1g-dev openjdk-11-jdk m4 libexempi-dev rsync texlive-full \
python3-numpy build-essential libsdl2-dev libjpeg-dev nasm tar libbz2-dev \
libgtk2.0-dev cmake libfluidsynth-dev libgme-dev libopenal-dev timidity \
libwildmidi-dev libboost-all-dev julia libsdl2-dev
出现问题:
解决:去掉julia重新执行,由于ubuntu下无julia软件包,所以安装如下:
下载:https://julialang.org/downloads/
安装:注意1.0和0.6版本的区别及使用
1.0版本文档:https://docs.julialang.org/en/v1/
解压:tar -zxvf julia-1.0.0-linux-x86_64.tar.gz -C /home/lln/software
创建软链接:sudo ln -s /home/lln/software/julia-1.0.0/bin/julia /bin/julia
3.install Bazel:
Bazel:https://docs.bazel.build/versions/master/install-ubuntu.html#installing-bazel-on-ubuntu
$ curl -L -o /tmp/bazel.sh https://github.com/bazelbuild/bazel/releases/download/0.14.1/bazel-0.14.1-installer-linux-x86_64.sh
$ sudo bash /tmp/bazel.sh && rm /tmp/bazel.sh
4.Build (all platforms)
a.Install the requirements which are common across platforms:
进入julia模式——>进入Pkg模式——>添加所需要的包
julia下按下]即进入Pkg,输入add CxxWrap。如下图:
b.Clone this project
$ git clone https://github.com/ChrisCummins/phd.git
$ cd phd
c.Configure the build and answer the yes/no questions. The default answers should be fine:
$ ./configure
d.set up the shell environment for running bazel. The file .env is created by the configure process and must be sourced for every shell we want to use bazel with:
$ source $PWD/.env
e.build or test whatever bazel targets you’d like. Use bazel query //… to list the available targets. E.g. to run the entire test suite, run:
$ bazel test //...
问题1:运行bazel query //… 问题2:运行运行bazel test //…
解决:安装pip3
sudo apt-get install python3-pip
再次运行时而出现以下异常时而出现之前的ERROR
socket.timeout:The read operation timed out
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host=‘files.pythonhosted.org’, port=443): Read timed out.
解决:
百度发现出现0 packages loaded问题是bazel的问题,参考链接中问题四:https://blog.csdn.net/qq_17130909/article/details/78637329
重新运行:bazel test -c opt --copt=-msse4 //...
出现以下问题:
docker 中执行
1.docker run -it ubuntu:18.04 /bin/bash
2.
$ apt-get update
$ apt install -y --no-install-recommends \
ca-certificates curl g++ git libmysqlclient-dev ocl-icd-opencl-dev \
pkg-config python python-dev python3.6 python3.6-dev python3-distutils \
unzip zip zlib1g-dev openjdk-11-jdk m4 libexempi-dev rsync texlive-full \
python3-numpy build-essential libsdl2-dev libjpeg-dev nasm tar libbz2-dev \
libgtk2.0-dev cmake libfluidsynth-dev libgme-dev libopenal-dev timidity \
libwildmidi-dev libboost-all-dev libsdl2-dev
julia的安装
安装wget:apt-get install wget
下载julia:
wget https://julialang-s3.julialang.org/bin/linux/x64/1.0/julia-1.0.0-linux-x86_64.tar.gz
解压:tar -xzvf julia-1.0.0-linux-x86_64.tar.gz
创建软链接:ln -s /julia-1.0.0/bin/julia /bin/julia
运行:julia
docker容器执行bazel test //...
结果如下:
luo:
docker容器执行bazel test //deeplearning/clgen/...
结果如下:
luo:
docker容器执行
bazel run //deeplearning/clgen -- \ --config $PWD/deeplearning/clgen/tests/data/tiny/config.pbtxt
结果如下:
docker容器执行docker run chriscummins/opencl_fuzz
结果如下:
服务器中运行出现:
luo:
Gated Graph Neural Network
1.安装python package rdkit(首先安装anaconda3)
安装anaconda3:
a.下载(最新版本):https://mirrors.tuna.tsinghua.edu.cn/anaconda/archive/
b.安装(打开下载位置,运行bash文件):运行 .sh 文件:
bash Anaconda3-5.3.0-Linux-x86_64.sh
- 进入注册信息页面,输入yes;
- 阅读注册信息,然后输入yes;
- 查看文件即将安装的位置,按enter,即可安装;
- 安装完成后,收到加入环境变量的提示信息,输入yes;
- 提示信息“Do you wish to proceed with the
installation of Microsoft VSCode? [yes|no]”,输入no;
c.重启终端,即可使用Anaconda3;
注意:忘记加入环境变量,执行:
vim ~/.bashrc
export PATH="/root/anaconda3/bin:$PATH"
d.卸载Anaconda3
删除整个anaconda目录:rm -rf /root/anaconda3
到根目录下,打开~/.bashrc:vim ~/.bashrc
用#号注释掉之前添加的路径(或直接删除):
#export PATH=/home/lq/anaconda3/bin:$PATH
使其立即生效:source ~/.bashrc
安装rdkit
conda install -c rdkit rdkit
2.获取数据执行get_data.py
python ./get_data.py
出现问题:
1.ImportError: libXrender.so.1: cannot open shared object file: No such file or directory
解决:安装libXrender
apt-get install libxrender1
2.ubuntu下ImportError: libXext.so.6: cannot open shared object file: No such file or directory
解决:安装libXext
apt-get install libxext-dev
(如果报找不到下载地址,先执行:apt-get update
)
结果:
3.run sparse Gated Graph Neural Networks:
python3 ./chem_tensorflow_sparse.py
结果: