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<h1 class="mume-header" id="fundamental-usage-of-linux">Fundamental usage of Linux</h1>
<h2 class="mume-header" id="0-computer-architech">0. Computer Architech</h2>
<img src="image/1.png">
<h2 class="mume-header" id="1-everything-is-a-file">1. Everything is a file</h2>
<img src="image/folder.jpg">
<h2 class="mume-header" id="2-command">2. Command</h2>
<img src="image/command.jpg">
<h3 class="mume-header" id="21-path-and-env">2.1 Path and env</h3>
<p><code>env</code> see the system path. All packages or executable file in path can be executed directly. Others must be executed by <code>./</code> and the absolute path.such as <code>./home/yongjian/execute/MC_multi_chian</code>.</p>
<p>type <code>env</code> or <code>echo $PATH</code>, you'll see<br>
<img src="image/path.jpg"></p>
<p>Every user has himself PATH, there are two methods. Modify <code>/etc/profile</code> for all user, <code>/home/${yourself}/.bashrc</code> for one user.</p>
<p><code>source /etc/profile</code> or <code>source /home/${yourself}/.bashrc</code> to refresh path.<br>
<img src="image/profile.jpg"><br>
<strong>SECURITY FIRST</strong></p>
<h3 class="mume-header" id="21-whereis-and-aptadvanced-packaging-tool">2.1 whereis and apt(Advanced Packaging Tool)</h3>
<p>Most fundamental applications can be found in <code>/usr/bin</code>, such as <code>python</code>,<code>mpirun</code>. If you want to use parallel computing, you can type <code>whereis mpirun</code>.<br>
<img src="image/whereis.jpg"><br>
If you are curious, use <code>ls -l</code> to show the detail of mpirun file.<br>
<img src="image/ls.jpg"><br>
Different color means different file types.<br>
<img src="image/color.png" width="200%"></p>
<p>Use <code>apt</code> install software or depends if there is.</p>
<p>fftw3 is a fundamental scientific computing library, <code>sudo apt install fftw3</code> is your better choice.</p>
<p><strong>I don't think that compiling every lib or application yourself is OK</strong></p>
<h2 class="mume-header" id="3-simulation-softwares">3 Simulation Softwares</h2>
<p>Lammps and Gromacs are installed in most machine, if you type <code>whereis lmp_stable</code> or <code>whereis lmp</code> or <code>whereis gmx</code> and don't find them, follow the installation on their official website.(some online tutorial maybe out of date)</p>
<h2 class="mume-header" id="4-file-system-and-mount">4 File system and mount</h2>
<p>chown chmod mount</p>
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