====== Notebook 环境搭建 ======
>[[stat:setupconda:packages]]
>[[stat:setupconda:speedtest]]

>SOS[[https://vatlab.github.io/sos-docs/running.html#r]]
>python包推荐[[https://github.com/jobbole/awesome-python-cn]]
>R包推荐[[https://github.com/qinwf/awesome-R]]
>机器学习包汇总[[https://github.com/josephmisiti/awesome-machine-learning/]]
>清华开源镜像[[https://mirror.tuna.tsinghua.edu.cn/help/]]

>MKL:[[https://software.intel.com/en-us/mkl]]



=====2 Anaconda安装=====
>用wget下载[[https://www.anaconda.com/download/#linux]]
>安装Anaconda[[http://docs.anaconda.com/anaconda/install/linux/]]
====2.1 安装====
<code>
wget https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh
bash Anaconda3-5.3.0-Linux-x86_64.sh
</code>
修改 ''~/.bashrc'' 将conda命令加入系统路径
<file>
__conda_setup="$(CONDA_REPORT_ERRORS=false '/home/conda/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
    \eval "$__conda_setup"
else
    if [ -f "/home/conda/etc/profile.d/conda.sh" ]; then
        . "/home/conda/etc/profile.d/conda.sh"
        CONDA_CHANGEPS1=false conda activate base
    else
        \export PATH="/home/conda/bin:$PATH"
    fi
fi
unset __conda_setup
</file>
====2.2 配置conda源====
配置文件地址 ''~/.condarc''
<file .condarc .condarc>
channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
ssl_verify: false
show_channel_urls: false
</file>
====2.3 Notebook配置文件====
[[https://blog.csdn.net/u014465934/article/details/80377470]] 中文支持
===2.3.1 使用 python 生成 hashed 密码===
<code>
from notebook.auth import passwd
from IPython.lib import passwd
passwd("jupyter")
</code>
===2.3.2 修改Notebook配置文件===
生成配置文件。
<code>
jupyter notebook --generate-config
</code>
找到 ''~/.jupyter/jupyter_notebook_config.py'' 并修改。
<file .py jupyter_notebook_config.py>
c.NotebookApp.password = u'sha1:d6ce897cf380:b3f6c684b2964a90f17865dfe4649ec70f9b3b4b'
c.NotebookApp.ip = '0.0.0.0'
c.NotebookApp.port = 11995
c.NotebookApp.open_browser = False
c.NotebookApp.token = ''
c.NotebookApp.allow_root = False
c.NotebookApp.notebook_dir = u'/home/notebook'
</file>
===查看安装的核心===
<code>
jupyter kernelspec list
</code>
====2.4 安装Conda常用包====
<code>
conda install -c mro r
conda install gcc_linux-64
conda install gxx_linux-64
conda install gfortran_linux-64
conda install -c intel mkl
conda install -c intel mkl-devel

pip install modin
conda install scikit-learn
conda install jupyter
conda install bokeh
conda install plotly
conda install matplotlib
conda install seaborn

conda install pytorch

conda install h2o
conda install xgboost
conda install lightbgm
</code>
==== 2.5 配置matplotlib ====
  - 放置中文字库文件至''/usr/share/font/truetype/''\\
  - ''fc-list :lang=zh''命令查看支持中文的字体名称\\
  - 清理''~/.cache/matplotlib''的字库列表缓存\\
  - 如下修改用户配置文件，在''~/.config/matplotlib''\\ 

<code>
font.size           : 20.0
font.family         : sans-serif
font.sans-serif     : SimHei, DejaVu Sans, Bitstream Vera Sans, Lucida Grande, Verdana, Geneva, Lucid, Arial, Helvetica, Avant Garde, sans-serif
axes.titlesize      : 24   
axes.labelsize      : 22  
axes.unicode_minus  : False   
xtick.labelsize      : 16 
ytick.labelsize      : 16 
legend.fontsize      : 20
figure.titlesize : 22     
figure.figsize   : 12, 8  
figure.dpi       : 300     
</code>
=====CRAN安装=====
[[https://linuxize.com/post/how-to-install-r-on-ubuntu-20-04/]]
<code>
apt install dirmngr gnupg apt-transport-https ca-certificates software-properties-common

apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'

apt install r-base

apt install build-essential
</code>
=====3 MRO安装=====
>微软MRO [[https://mran.microsoft.com/|MRO]]
>R原版清华加速镜像[[https://mirrors.tuna.tsinghua.edu.cn/CRAN/]]
>MKL with R[[https://software.intel.com/en-us/articles/using-intel-mkl-with-r]]
>[[https://software.intel.com/en-us/articles/extending-r-with-intel-mkl]]
>[[https://software.intel.com/en-us/articles/quick-linking-intel-mkl-blas-lapack-to-r]]
>[[https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Shared-BLAS]]

进入R安装pkg ''/opt/microsoft/ropen/3.4.3/lib64/R/bin/R''
===安装命令===
<code>
tar -xf microsoft-r-open-3.5.3.tar.gz
cd microsoft-r-open/
sudo ./install.sh
</code>
====Build with mkl====
<code>
apt install gfortran-9 icu-devtools libblas-dev libblas3 libbz2-dev libfile-basedir-perl libfile-desktopentry-perl  libfile-mimeinfo-perl libfontenc1 libgfortran-9-dev libgfortran5 libicu-dev libio-stringy-perl libipc-system-simple-perl libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblapack3 liblzma-dev libnet-dbus-perl libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpng-dev libpng-tools libtcl8.6 libtie-ixhash-perl libtk8.6 libx11-protocol-perl libxaw7 libxcomposite1 libxft2 libxkbfile1 libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl libxmu6 libxpm4 libxtst6 libxxf86dga1
apt install libxt-dev libcairo2-dev

source /opt/intel/compilers_and_libraries_2020.1.217/linux/bin/compilervars.sh intel64
MKL="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl "

./configure --with-blas="$MKL" --with-lapack --enable-memory-profiling --with-libpng --with-jpeglib --with-libtiff --with-cairo --with-recommended-packages=no --with-x=no --enable-R-shlib

make -j4
make -j4 cairodevices 

</code>
===检查===
<code>
capabilities()
</code>
====配置R的源====
修改文件 ''~/.Rprofile''
<file .Rprofile .Rprofile>
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")

options("repos" = c(CRAN="https://mirrors.aliyun.com/CRAN/"))
options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
options(Ncpus = 8)
#options(bitmapType='cairo')
#Sys.setenv("DISPLAY"=":0")
#options(device = null_device)
</file>
或直接在R中选择镜像
<code>
chooseCRANmirror()
chooseBioCmirror()
</code>
====3.1 安装IRkernel====
Jupyter的R核心库：[[https://irkernel.github.io/installation/]]\\
<code>
update.packages(ask = FALSE)  #更新所有包

update.packages(checkBuilt = TRUE, ask = FALSE)  #更新R后检查包是否需要重新安装

install.packages('IRkernel')
IRkernel::installspec()
IRkernel::installspec(user=FALSE)
IRkernel::installspec(name = 'Rmkl', displayname = 'R-mkl')


install.packages("openssl")
install.packages('devtools')
devtools::install_github('IRkernel/IRkernel')

install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'uuid', 'digest')) #报错备用
devtools::install_git("https://github.com/IRkernel/IRkernel.git", ref = "master")   #报错备用

install.packages("caTools", repo=http://mirrors.tuna.tsinghua.edu.cn/CRAN/)
</code>

====3.2 安装常用包====
<code>
install.packages("tidyverse")


install.packages('agricolae')
install.packages('bigmemory')
install.packages('car')
install.packages("Cairo")
install.packages('caret')
install.packages('DMwR')
install.packages("dplyr")
install.packages("data.table")
install.packages('doParallel')

install.packages('energy')
install.packages('future')
install.packages('forecastHybrid')
install.packages('glmnet')
install.packages('ggplot2')
install.packages('gbm')
install.packages('h2o')
install.packages('mlr3')
install.packages('multcomp')
install.packages('mcmc')
install.packages('psych')
install.packages('prophet')
install.packages('Rcpp')
install.packages('randomForest')
install.packages('randomForestSRC')
install.packages('rdetools')
install.packages("reshape2")
install.packages("readr")
install.packages("SuppDists")
install.packages("utf8")
install.packages('xgboost')

</code>
[[https://github.com/tidyverse/haven/issues/363]]
====安装Bioconductor====
>官网[[https://www.bioconductor.org/]]
<code>
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))
BiocManager::install(c("DOSE","clusterProfiler","enrichplot","org.Rn.eg.db","org.Mm.eg.db","AnnotationDbi"))
BiocManager::install("DESeq2")
</code>
====测试====
[[https://blog.csdn.net/byplane/article/details/51742048]]
<code>
system.time(matrix(rnorm(4096*4096), nrow=4096, ncol=4096) %*% matrix(rnorm(4096*4096), nrow=4096, ncol=4096))

LD_PRELOAD=/usr/local/cuda-10.0/lib64/libnvblas.so NVBLAS_CONFIG_FILE=/etc/nvblas.conf R


LD_PRELOAD=/usr/local/cuda-10.0/lib64/libnvblas.so NVBLAS_CONFIG_FILE=/etc/nvblas.conf Rscript
</code>




=====5 安装Cuda=====
启动代码[[https://gist.github.com/cheuerde/fe11d1b97193650a00a3]]
[[https://clint.id.au/?p=1900]]
jupyterhub[[https://www.cnblogs.com/crxis/p/9078278.html]]