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installation.html
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<title>Install Software in Cluster</title>
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<h1>Install Software in Cluster</h1>
</div>
<p>In default situation, user cannot install software via <tt>root</tt> authority. However, user can install their needed software under their own <tt><i>home</i>user_name</tt> directory. Here are some example:</p>
<h3>Install Python via Anaconda:</h3>
<p>Conda can create a virtual python environment, and it easily install packages. This created virtual individual environment can solve the python's version and requirement problem and it is fully controlled by the user <a href="">you can install packages without root permission</a></p>
<ol>
<li><p>Activate <tt>Anaconda</tt> PATH</p>
</li>
<li><p>Create an environment with <tt>conda</tt></p>
</li>
<li><p>Use <tt>conda</tt> or <tt>pip</tt> to install packages </p>
</li>
</ol>
<div class="codeblock">
<div class="blocktitle">Create local Python Environment with Conda</div>
<div class="blockcontent"><pre>
# activate anaconda PATH
module load computing/conda/5.3.1
# using conda
proxychains4 conda create -name=DeepLearning python=3.7
# activate DeepLearning environment via conda
source activate DeepLearning (or conda activate DeepLearning)
# use Beigjing Foreign Studies Univerisy's Mirrors (https://mirrors.bfsu.edu.cn)
proxychains4 python -m pip config set global.index-url https://mirrors.bfsu.edu.cn/pypi/web/simple
## run program
python main.py
</pre></div></div>
<div class="infoblock">
<div class="blockcontent">
<p>Remember to use <tt>proxychains4</tt> to do the download or run the programme which needs internet connection.</p>
</div></div>
<h3>Install R via Anaconda:</h3>
<p>Conda can create a virtual python environment, and it easily install packages. This created virtual individual environment can solve the python's version and requirement problem and it is fully controlled by the user <a href="">you can install packages without root permission</a></p>
<ol>
<li><p>Activate <tt>Anaconda</tt> environment</p>
</li>
<li><p>Create an environment with <tt>conda</tt></p>
</li>
</ol>
<div class="codeblock">
<div class="blocktitle">Create local R Environment with Conda</div>
<div class="blockcontent"><pre>
# activate anaconda PATH
module load computing/conda/5.3.1
# using conda
proxychains4 conda create -n=r4-base
source activate r4-base
proxychains4 conda install -c conda-forge r-base #or proxychains4 conda install -c conda-forge/label/gcc7 r-base
# or proxychains4 conda install r-base
## run program
R
</pre></div></div>
<p><tt>Tips:</tt> sometimes we may use <tt>devtools::install_github()</tt> to install R pacakge directly from GitHub, however, the connection between the school intranet and GitHub server is not robust enough. Here is a solution:</p>
<div class="infoblock">
<div class="blocktitle">install package via the github proxy</div>
<div class="blockcontent">
<p>remotes::install_git(“https:<i></i>github.com.cnpmjs.org<i>GuangchuangYu</i>nCov2019”)
devtools::install_git(“https:<i></i>github.com.cnpmjs.org<i>GuangchuangYu</i>nCov2019”)</p>
</div></div>
<p>You may use <a href="https://mirrors.bfsu.edu.cn"> BFSU Mirrors</a> to accelerate R package installation:</p>
<div class="codeblock">
<div class="blocktitle">use BFSU CRAN mirrors</div>
<div class="blockcontent"><pre>
# add this command to your ~/.Rprofile
options("repos" = c(CRAN="https://mirrors.bfsu.edu.cn/CRAN/"))
# or, install pakcages with this options
install.packages("{package_name}", repos="https://mirrors.bfsu.edu.cn/CRAN/")
</pre></div></div>
<h3>Install Julia via Anaconda:</h3>
<ol>
<li><p>Activate <tt>Anaconda</tt> PATH</p>
</li>
<li><p>Create an environment with <tt>conda</tt></p>
</li>
</ol>
<div class="codeblock">
<div class="blocktitle">Create local Julia Environment with Conda</div>
<div class="blockcontent"><pre>
# activate anaconda PATH
module load computing/conda/5.3.1
# using conda
proxychains4 conda create -name=julia_env julia
</pre></div></div>
<p>You may use <a href="https://mirrors.bfsu.edu.cn"> BFSU Mirrors</a> to accelerate R package installation:</p>
<div class="codeblock">
<div class="blocktitle">use BFSU CRAN mirrors</div>
<div class="blockcontent"><pre>
# add this command to your ~/.bashrc
export JULIA_PKG_SERVER=https://mirrors.bfsu.edu.cn/julia
# or, install use JuliaZH (package) to change mirrors
add JuliaZH # install `JuliaZU`
using JuliaZH # when using, it will automatically switch to the China's mirrors
JuliaZH.set_mirror("BFSU") # You can also mannually switch to BFSU mirror
JuliaZH.mirrors # Query the upstream information
</pre></div></div>
<h3>Install packages wihout sudo privileges</h3>
<p>User withou sudo priviledges need to compile the package from source, for example:</p>
<div class="codeblock">
<div class="blocktitle">install from source</div>
<div class="blockcontent"><pre>
apt-get source PACKAGE
./configure --prefix=$HOME/{package-PATH}
make
make install
</pre></div></div>
<h3>Anaconda mirrors</h3>
<p>You can use these mirrors in case the BFSU's is down:</p>
<ul>
<li><p><a href="https://mirrors.bfsu.edu.cn/">Tsinghua (tuna) Open Source Mirrors</a></p>
</li>
<li><p><a href="https://mirrors.sustech.edu.cn/">SUSTech Open Source Mirrors</a></p>
</li>
<li><p><a href="https://mirror.bjtu.edu.cn/">BJTU free and open source software mirror</a></p>
</li>
</ul>
<p>Please follow their instructions and modify your configuration.</p>
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