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This repository provides User Manual for setting up a Docker environment tailored for testing DGTD code.
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<section id="user-manual-windows-system">
<h1>User Manual (Windows System)<a class="headerlink" href="#user-manual-windows-system" title="Link to this heading"></a></h1>
<section id="step-by-step-installation-in-windows">
<h2>Step-by-Step installation in Windows<a class="headerlink" href="#step-by-step-installation-in-windows" title="Link to this heading"></a></h2>
<p>Welcome to the user manual for setting up and using Docker on a Windows system. This guide will provide comprehensive instructions to help you install and configure Docker Desktop on Windows, activate virtualization in BIOS, install WSL (Windows Subsystem for Linux), import Docker images, mount user data, and run Docker containers. Additionally, it includes pointers and tips to address common questions and issues that users may encounter.</p>
</section>
<section id="activate-virtualization-in-bios">
<h2>Activate Virtualization in BIOS<a class="headerlink" href="#activate-virtualization-in-bios" title="Link to this heading"></a></h2>
<p>To enable virtualization, you’ll need to access the BIOS settings during startup. Here’s how:</p>
<ol class="arabic simple">
<li><p>Power on your computer.</p></li>
<li><p>Keep an eye on the initial boot screen.</p></li>
<li><p>When you see the screen, press the <code class="docutils literal notranslate"><span class="pre">F2</span> <span class="pre">/</span> <span class="pre">F10</span> <span class="pre">/</span> <span class="pre">F12</span> <span class="pre">/</span> <span class="pre">Esc</span> <span class="pre">/</span> <span class="pre">Delete</span> <span class="pre">/</span> <span class="pre">Enter</span></code> key to enter the BIOS settings.</p></li>
</ol>
<figure class="align-center" id="id1">
<a class="reference internal image-reference" href="_images/B1.jpg"><img alt="_images/B1.jpg" src="_images/B1.jpg" style="width: 900px;" /></a>
<figcaption>
<p><span class="caption-text">Screen when we boot up the machine. Press <code class="docutils literal notranslate"><span class="pre">F2</span> <span class="pre">/</span> <span class="pre">F10</span> <span class="pre">/</span> <span class="pre">F12</span> <span class="pre">/</span> <span class="pre">Esc</span> <span class="pre">/</span> <span class="pre">Delete</span> <span class="pre">/</span> <span class="pre">Enter</span></code></span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Once inside the BIOS settings:</p>
<ol class="arabic simple" start="4">
<li><p>Navigate through the BIOS menus using the arrow keys. Look for the section typically labeled <code class="docutils literal notranslate"><span class="pre">Advanced</span></code>, <code class="docutils literal notranslate"><span class="pre">Advanced</span> <span class="pre">Settings</span></code> or <code class="docutils literal notranslate"><span class="pre">CPU</span> <span class="pre">Configuration</span></code>.</p></li>
</ol>
<p>or</p>
<ol class="arabic simple" start="4">
<li><p>Alternatively, some BIOS versions allow you to search for settings. Look for a search bar or a similar feature where you can type <code class="docutils literal notranslate"><span class="pre">virtualization</span></code> or <code class="docutils literal notranslate"><span class="pre">VT-x</span></code> (for Intel processors) / <code class="docutils literal notranslate"><span class="pre">AMD-V</span></code> (for AMD processors).</p></li>
</ol>
<figure class="align-center" id="id2">
<a class="reference internal image-reference" href="_images/B3.jpg"><img alt="_images/B3.jpg" src="_images/B3.jpg" style="width: 900px;" /></a>
<figcaption>
<p><span class="caption-text">BIOS settings screen.</span><a class="headerlink" href="#id2" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Once you locate the virtualization options within these sections, you can proceed to enable them. This step is crucial for utilizing virtualization features such as running virtual machines or other virtualization-based applications on your computer. After making the necessary changes, remember to save your settings and exit the BIOS.</p>
<ol class="arabic simple" start="5">
<li><p>Change the setting from <code class="docutils literal notranslate"><span class="pre">Disabled</span></code> to <code class="docutils literal notranslate"><span class="pre">Enabled</span></code> using the appropriate key (usually <code class="docutils literal notranslate"><span class="pre">Enter</span></code> or the <code class="docutils literal notranslate"><span class="pre">+</span></code> key).</p></li>
<li><p>Save changes and exit BIOS</p></li>
</ol>
<figure class="align-center" id="id3">
<a class="reference internal image-reference" href="_images/B2.jpg"><img alt="_images/B2.jpg" src="_images/B2.jpg" style="width: 900px;" /></a>
<figcaption>
<p><span class="caption-text">Turn on Virtualization.</span><a class="headerlink" href="#id3" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Your computer will restart with virtualization support enabled.</p>
</section>
<section id="install-wsl">
<h2>Install WSL<a class="headerlink" href="#install-wsl" title="Link to this heading"></a></h2>
<p>Here are the simplified instructions for installing Windows Subsystem for Linux (WSL) and verifying its installation:</p>
<p><strong>Installing Windows Subsystem for Linux (WSL)</strong></p>
<ol class="arabic simple">
<li><p><strong>Open PowerShell as Administrator</strong></p></li>
<li><p><strong>Install WSL:</strong>
Run the following command to install WSL: <code class="docutils literal notranslate"><span class="pre">wsl</span> <span class="pre">--install</span></code>.
Follow any prompts or confirmations that appear during the installation process.</p></li>
<li><p><strong>Wait for Installation to Complete:</strong>
Allow the installation process to finish. This may take some time depending on your internet speed.</p></li>
</ol>
<figure class="align-center" id="id4">
<a class="reference internal image-reference" href="_images/W3.png"><img alt="_images/W3.png" src="_images/W3.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Install Windows Subsystem for Linux (WSL)</span><a class="headerlink" href="#id4" title="Link to this image"></a></p>
</figcaption>
</figure>
<ol class="arabic simple" start="4">
<li><p><strong>Check WSL Version:</strong>
Run the following command to check the installed WSL versions and their respective distributions: <code class="docutils literal notranslate"><span class="pre">wsl</span> <span class="pre">-l</span> <span class="pre">-v</span></code>
This command lists all installed Linux distributions and their associated WSL versions (<cite>1</cite> or <cite>2</cite>).</p></li>
</ol>
<figure class="align-center" id="id5">
<a class="reference internal image-reference" href="_images/W4.png"><img alt="_images/W4.png" src="_images/W4.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Check if WSL is properly installed</span><a class="headerlink" href="#id5" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Following these steps ensures that you install Windows Subsystem for Linux (WSL) and confirm its proper installation on your Windows system.</p>
</section>
<section id="install-docker-desktop-in-windows">
<h2>Install Docker Desktop in Windows<a class="headerlink" href="#install-docker-desktop-in-windows" title="Link to this heading"></a></h2>
<ol class="arabic simple">
<li><p>Download Docker Desktop from <a class="reference external" href="https://www.docker.com/get-started/">Docker’s official website</a> (<a class="reference external" href="https://www.docker.com/get-started/">https://www.docker.com/get-started/</a>).</p></li>
</ol>
<figure class="align-center" id="id6">
<a class="reference internal image-reference" href="_images/W5.png"><img alt="_images/W5.png" src="_images/W5.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Download Docker Desktop online</span><a class="headerlink" href="#id6" title="Link to this image"></a></p>
</figcaption>
</figure>
<ol class="arabic simple" start="2">
<li><p>Once downloaded, locate the installer file (e.g., <code class="docutils literal notranslate"><span class="pre">DockerDesktopInstaller.exe</span></code>) and double-click to launch it.</p></li>
<li><p>Follow the prompts provided by the Docker Desktop installer to complete the installation process. This may involve accepting terms and conditions and choosing installation preferences.</p></li>
</ol>
<figure class="align-center" id="id7">
<a class="reference internal image-reference" href="_images/W6.png"><img alt="_images/W6.png" src="_images/W6.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Docker Desktop Installer</span><a class="headerlink" href="#id7" title="Link to this image"></a></p>
</figcaption>
</figure>
<figure class="align-center" id="id8">
<a class="reference internal image-reference" href="_images/W7.png"><img alt="_images/W7.png" src="_images/W7.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Installing Docker Desktop</span><a class="headerlink" href="#id8" title="Link to this image"></a></p>
</figcaption>
</figure>
<figure class="align-center" id="id9">
<a class="reference internal image-reference" href="_images/W8.png"><img alt="_images/W8.png" src="_images/W8.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Finish installing Docker Desktop</span><a class="headerlink" href="#id9" title="Link to this image"></a></p>
</figcaption>
</figure>
<ol class="arabic simple" start="4">
<li><p>After installation, a Docker Desktop shortcut will appear on your desktop. The necessary components to run Maxwell-TD Docker images include Docker Desktop itself, Windows PowerShell for running CLI commands, and a designated working folder containing Docker images and user data (e.g., geometry information).</p></li>
</ol>
<figure class="align-center" id="id10">
<a class="reference internal image-reference" href="_images/W9.png"><img alt="_images/W9.png" src="_images/W9.png" style="width: 300px;" /></a>
<figcaption>
<p><span class="caption-text">All the data/folders/apps needed to run Maxwell-TD Docker image</span><a class="headerlink" href="#id10" title="Link to this image"></a></p>
</figcaption>
</figure>
<ol class="arabic simple" start="5">
<li><p>Launch Docker Desktop by double-clicking the Docker Desktop shortcut on your desktop.</p></li>
<li><p>Upon first launch, Docker Desktop may prompt you to accept terms and conditions. Agree to proceed with using the application.</p></li>
</ol>
<figure class="align-center" id="id11">
<a class="reference internal image-reference" href="_images/W10.png"><img alt="_images/W10.png" src="_images/W10.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Accept the terms and conditions</span><a class="headerlink" href="#id11" title="Link to this image"></a></p>
</figcaption>
</figure>
<ol class="arabic simple" start="7">
<li><p>You can continue without logging into Docker Desktop if prompted, and optionally skip any survey presented during initial setup.</p></li>
</ol>
<figure class="align-center" id="id12">
<a class="reference internal image-reference" href="_images/W11.png"><img alt="_images/W11.png" src="_images/W11.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Continue without logging in</span><a class="headerlink" href="#id12" title="Link to this image"></a></p>
</figcaption>
</figure>
<figure class="align-center" id="id13">
<a class="reference internal image-reference" href="_images/W12.png"><img alt="_images/W12.png" src="_images/W12.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Skip Survey</span><a class="headerlink" href="#id13" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Currently, the local repository in Docker Desktop is empty. To proceed, we must upload the compiled image for Maxwell-TD. This requires using the PowerShell console, as the GUI does not support managing local Docker images directly and defaults to searching online repositories for Docker images.</p>
<figure class="align-center" id="id14">
<a class="reference internal image-reference" href="_images/W13.png"><img alt="_images/W13.png" src="_images/W13.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Image local Repository</span><a class="headerlink" href="#id14" title="Link to this image"></a></p>
</figcaption>
</figure>
</section>
<section id="import-docker-image">
<h2>Import Docker Image<a class="headerlink" href="#import-docker-image" title="Link to this heading"></a></h2>
<p>Next, we need to mount the zipped Docker image onto the Windows system. Since this action cannot be performed using the Docker Desktop GUI, we’ll need to use the console terminal instead.</p>
<p>In the designated working folder, you will find a zipped Docker image file and an “examples” folder containing user-defined data.</p>
<figure class="align-center" id="id15">
<a class="reference internal image-reference" href="_images/W14.png"><img alt="_images/W14.png" src="_images/W14.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Location of Maxwell-TD Docker Image (Zipped)</span><a class="headerlink" href="#id15" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>To load the Docker image, execute the command <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">load</span> <span class="pre">--input</span> <span class="pre">&lt;PATH</span> <span class="pre">to</span> <span class="pre">zipped</span> <span class="pre">docker</span> <span class="pre">image&gt;</span></code>. This process will take some time, and you can verify its completion by using <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">images</span></code> in the console.</p>
<figure class="align-center" id="id16">
<a class="reference internal image-reference" href="_images/W16.png"><img alt="_images/W16.png" src="_images/W16.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Load and check Docker Image</span><a class="headerlink" href="#id16" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>The loaded Docker image will also be visible both in Docker Desktop.</p>
<figure class="align-center" id="id17">
<a class="reference internal image-reference" href="_images/W17.png"><img alt="_images/W17.png" src="_images/W17.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Loaded Docker Image can be seen in Docker Desktop</span><a class="headerlink" href="#id17" title="Link to this image"></a></p>
</figcaption>
</figure>
</section>
<section id="mounting-user-data-and-running-docker-image">
<h2>Mounting User data and running Docker image<a class="headerlink" href="#mounting-user-data-and-running-docker-image" title="Link to this heading"></a></h2>
<p>Finally, we are ready to run the Docker image. You can use a PowerShell script with administrative privileges to execute the Docker image. We have prepared a script file named <code class="docutils literal notranslate"><span class="pre">runDocker.ps1</span></code> that can be executed in the console terminal.</p>
<p>To run the script and start the Docker image, follow these steps:</p>
<ol class="arabic simple">
<li><p><strong>Open PowerShell as Administrator</strong></p></li>
<li><p><strong>Navigate to Script Directory:</strong>
Use the <code class="docutils literal notranslate"><span class="pre">cd</span></code> command to navigate to the directory where <code class="docutils literal notranslate"><span class="pre">runDocker.ps1</span></code> is located.</p></li>
<li><dl class="simple">
<dt><strong>Execute the Script:</strong></dt><dd><ul class="simple">
<li><p>Run the script by typing <code class="docutils literal notranslate"><span class="pre">.\runDocker.ps1</span></code> and press <code class="docutils literal notranslate"><span class="pre">Enter</span></code>.</p></li>
<li><p>The script will mount the folder containing user-defined data into the Docker Server environment.</p></li>
</ul>
</dd>
</dl>
</li>
</ol>
<div class="admonition note">
<p class="admonition-title">Note</p>
<ul class="simple">
<li><p>When running the Docker image, any data saved onto the mounted filesystem will persist. However, other modifications, such as custom installations of packages, will be temporary and will disappear after you exit the Docker session.</p></li>
<li><p>Treat the Docker image as a saved state of a customized environment.</p></li>
</ul>
</div>
<figure class="align-center" id="id18">
<a class="reference internal image-reference" href="_images/W18.png"><img alt="_images/W18.png" src="_images/W18.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Use PowerShell Script to run Docker Image</span><a class="headerlink" href="#id18" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Let’s break down the lines in the PowerShell script to understand the necessary steps for running the Docker image. This will clarify what is needed for execution.</p>
<ul class="simple">
<li><p><strong>$imageName</strong>:</p></li>
</ul>
<p>This variable defines the name of the Docker image that you want to run. In this case, it is set to <code class="docutils literal notranslate"><span class="pre">maxwell_td_image</span></code>. Users should not change this variable if they intend to run Maxwell-TD.</p>
<ul class="simple">
<li><p><strong>$containerName</strong>:</p></li>
</ul>
<p>This variable specifies the name of the container that will run the Docker image. You can run multiple containers from the same image concurrently, so each running instance needs a unique name. Users can customize this variable to suit their naming conventions.</p>
<ul class="simple">
<li><p><strong>$hostVolumePath</strong>:</p></li>
</ul>
<p>This variable holds the path to the working folder on the Windows system. This folder contains essential files such as geometry files for simulation models and scripts for setting simulation parameters. Users must update this path to point to their specific working folder.</p>
<ul class="simple">
<li><p><strong>$containerVolumePath</strong>:</p></li>
</ul>
<p>This variable defines the path within the Docker container (running on Linux environment) where the host volume (<strong>$hostVolumePath</strong>) will be mounted. In this script, it is set to <code class="docutils literal notranslate"><span class="pre">/dgtd/model/</span></code>. It is recommended that users do not change this variable unless necessary, to ensure compatibility with the Docker image’s expected mount point.</p>
<figure class="align-center" id="id19">
<a class="reference internal image-reference" href="_images/W20.png"><img alt="_images/W20.png" src="_images/W20.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">User-defined parameters to change location of User data</span><a class="headerlink" href="#id19" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Next, the script proceeds to execute several commands to display the paths and names. It also checks the CUDA version installed on the Windows device. Afterward, it runs the Docker command <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">run</span> <span class="pre">--rm</span> <span class="pre">--gpus</span> <span class="pre">all</span> <span class="pre">-it</span> <span class="pre">--name</span> <span class="pre">${containerName}</span> <span class="pre">-v</span> <span class="pre">${hostVolumePath}:${containerVolumePath}</span> <span class="pre">${imageName}</span></code>.</p>
<dl class="simple">
<dt><strong>Explanation of Docker Command Flags</strong></dt><dd><ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">run</span></code>: This command starts a new Docker container.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">--rm</span></code>: Automatically removes the container when it exits. Useful for temporary containers.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">--gpus</span> <span class="pre">all</span></code>: Enables access to all GPUs in the container.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">-it</span></code>: Allocates a pseudo-TTY and keeps stdin open. Allows interactive terminal access.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">--name</span> <span class="pre">${containerName}</span></code>: Assigns a name to the container instance based on the value stored in the <code class="docutils literal notranslate"><span class="pre">$containerName</span></code> variable.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">-v</span> <span class="pre">${hostVolumePath}:${containerVolumePath}</span></code>: Mounts a volume from the host machine (Windows) into the Docker container. <code class="docutils literal notranslate"><span class="pre">${hostVolumePath}</span></code> is the path on the host system, and <code class="docutils literal notranslate"><span class="pre">${containerVolumePath}</span></code> is the path inside the container where the volume will be mounted.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">${imageName}</span></code>: Specifies the Docker image to use for creating the container.</p></li>
</ul>
</dd>
<dt><strong>Additional Information</strong></dt><dd><ul class="simple">
<li><p>The <code class="docutils literal notranslate"><span class="pre">--rm</span></code> flag ensures that the container is automatically removed after it stops running, helping to manage resources efficiently.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">--gpus</span> <span class="pre">all</span></code> allows the Docker container to access all available GPUs on the host machine, which is crucial for applications that require GPU acceleration.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">-it</span></code> enables interactive mode with a terminal session, which is useful for interacting directly with the container if needed.</p></li>
</ul>
</dd>
</dl>
<p>This Docker command, when executed within the PowerShell script, sets up and runs the Docker container named <code class="docutils literal notranslate"><span class="pre">${containerName}</span></code> with GPU support, mounts necessary volumes, and utilizes the specified Docker image <code class="docutils literal notranslate"><span class="pre">${imageName}</span></code> for the Maxwell-TD application. Adjust <code class="docutils literal notranslate"><span class="pre">${containerName}</span></code>, <code class="docutils literal notranslate"><span class="pre">${hostVolumePath}</span></code>, <code class="docutils literal notranslate"><span class="pre">${containerVolumePath}</span></code>, and <code class="docutils literal notranslate"><span class="pre">${imageName}</span></code> as per your specific environment and requirements.</p>
<figure class="align-center" id="id20">
<a class="reference internal image-reference" href="_images/W21.png"><img alt="_images/W21.png" src="_images/W21.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Commands to run Docker image</span><a class="headerlink" href="#id20" title="Link to this image"></a></p>
</figcaption>
</figure>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>When opening a Windows text file in a Unix environment, extra <code class="docutils literal notranslate"><span class="pre">\r</span></code> characters at the end of each line can cause errors such as <code class="docutils literal notranslate"><span class="pre">/bin/bash^M:</span> <span class="pre">bad</span> <span class="pre">interpreter:</span> <span class="pre">No</span> <span class="pre">such</span> <span class="pre">file</span> <span class="pre">or</span> <span class="pre">directory</span></code>. This is because Unix-based systems expect lines to end with <code class="docutils literal notranslate"><span class="pre">\n</span></code> (newline) instead of <code class="docutils literal notranslate"><span class="pre">\r\n</span></code> (carriage return followed by newline) used in Windows.</p>
<p>To fix this issue, you can convert the line endings from Windows format to Unix format using utilities like <code class="docutils literal notranslate"><span class="pre">dos2unix</span></code>, which removes the extra <code class="docutils literal notranslate"><span class="pre">\r</span></code> characters. Alternatively, you can use the included function <code class="docutils literal notranslate"><span class="pre">Remove-CarriageReturns</span></code> in <code class="docutils literal notranslate"><span class="pre">runDocker.ps1</span></code> to process the files. Once corrected, your script should execute correctly within Docker or any Unix-based environment without encountering interpreter errors.</p>
</div>
<figure class="align-center" id="id21">
<a class="reference internal image-reference" href="_images/W19.png"><img alt="_images/W19.png" src="_images/W19.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Miscellaneous function to treat textfiles from Windows System (Optional)</span><a class="headerlink" href="#id21" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>To run the script, navigate to the directory where <code class="docutils literal notranslate"><span class="pre">runDocker.ps1</span></code> is located and execute <code class="docutils literal notranslate"><span class="pre">./runDocker.ps1</span></code>. The script will display the CUDA toolkit version and open a BASH shell in the Docker container with <code class="docutils literal notranslate"><span class="pre">maxwell_td_image</span></code>. This environment simulates a Linux environment.</p>
<figure class="align-center" id="id22">
<a class="reference internal image-reference" href="_images/W27.png"><img alt="_images/W27.png" src="_images/W27.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Running PowerShell Script</span><a class="headerlink" href="#id22" title="Link to this image"></a></p>
</figcaption>
</figure>
</section>
<section id="how-to-use-maxwell-td">
<h2>How to use Maxwell-TD<a class="headerlink" href="#how-to-use-maxwell-td" title="Link to this heading"></a></h2>
<p>Upon starting the Docker container, you will be in the <code class="docutils literal notranslate"><span class="pre">/dgtd/</span></code> directory, where the Discontinuous Galerkin Time-Domain (DGTD) code is located. The compiled code can be found in the <code class="docutils literal notranslate"><span class="pre">/dgtd/build/</span></code> directory, with the executables named <code class="docutils literal notranslate"><span class="pre">maxwelltd_CUDA_LTS_DOUBLEpre_FLOATpro</span></code> and <code class="docutils literal notranslate"><span class="pre">maxwelltd_CUDA_LTS_DOUBLEpre_FLOATpro-</span></code>. User data, mounted from the Windows filesystem, is available in the <code class="docutils literal notranslate"><span class="pre">/dgtd/model/</span></code> directory. Before running the simulation, the compiled executable must be copied to the simulation folder (<code class="docutils literal notranslate"><span class="pre">/dgtd/model/MaxwellTD_data/</span></code>). This can be done by executing the following command:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>/dgtd/build/maxwelltd_CUDA_LTS_DOUBLEpre_FLOATpro*<span class="w"> </span>/dgtd/model/MaxwellTD_data/
</pre></div>
</div>
<figure class="align-center" id="id23">
<a class="reference internal image-reference" href="_images/W29.png"><img alt="_images/W29.png" src="_images/W29.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Local Directory in Docker Image</span><a class="headerlink" href="#id23" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Simulation files for the MaxwellTD model are located in the directory <code class="docutils literal notranslate"><span class="pre">/dgtd/model/MaxwellTD_data</span></code>. Additionally, we have included CST reference data for the same simulation model in the folder <code class="docutils literal notranslate"><span class="pre">CST_data</span></code>. A Python script named <code class="docutils literal notranslate"><span class="pre">compare_maxwelltd_CST.py</span></code> has been provided to facilitate extraction and comparison of data between the DGTD simulation and CST data.</p>
<figure class="align-center" id="id24">
<a class="reference internal image-reference" href="_images/W31a.png"><img alt="_images/W31a.png" src="_images/W31a.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Simulation folder</span><a class="headerlink" href="#id24" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>To run the DGTD simulation, we can navigate to <code class="docutils literal notranslate"><span class="pre">/dgtd/model/MaxwellTD_data/</span></code> and run the shell script <code class="docutils literal notranslate"><span class="pre">CUDA_LTS_RUN.sh</span></code>.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./CUDA_LTS_RUN.sh
</pre></div>
</div>
<figure class="align-center" id="id25">
<a class="reference internal image-reference" href="_images/W45.png"><img alt="_images/W45.png" src="_images/W45.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Running Simulation script</span><a class="headerlink" href="#id25" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>This will initiate the DGTD simulation.</p>
<figure class="align-center" id="id26">
<a class="reference internal image-reference" href="_images/W46.png"><img alt="_images/W46.png" src="_images/W46.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Simulating running</span><a class="headerlink" href="#id26" title="Link to this image"></a></p>
</figcaption>
</figure>
<figure class="align-center" id="id27">
<a class="reference internal image-reference" href="_images/W47.png"><img alt="_images/W47.png" src="_images/W47.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">End of simulation</span><a class="headerlink" href="#id27" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Following the completion of the simulation, you can execute the Python script <code class="docutils literal notranslate"><span class="pre">compare_maxwelltd_CST.py</span></code> to compare the results with those obtained from the CST simulation.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python3<span class="w"> </span>compare_maxwelltd_CST.py
</pre></div>
</div>
<figure class="align-center" id="id28">
<a class="reference internal image-reference" href="_images/W49.png"><img alt="_images/W49.png" src="_images/W49.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Running post-processing PYTHON script</span><a class="headerlink" href="#id28" title="Link to this image"></a></p>
</figcaption>
</figure>
</section>
<section id="common-issues">
<h2>Common issues<a class="headerlink" href="#common-issues" title="Link to this heading"></a></h2>
<section id="incompatible-gpu-drivers-toolkit">
<h3>Incompatible GPU drivers/toolkit<a class="headerlink" href="#incompatible-gpu-drivers-toolkit" title="Link to this heading"></a></h3>
<p>It’s essential to verify that your Windows device has the correct CUDA toolkit installed to run Maxwell-TD. You can check the CUDA toolkit version by using ‘nvidia-smi’ in the console terminal. The minimum required version to run Maxwell-TD is CUDA toolkit 12.4.</p>
<figure class="align-center" id="id29">
<a class="reference internal image-reference" href="_images/W22.png"><img alt="_images/W22.png" src="_images/W22.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Check CUDA toolkit version</span><a class="headerlink" href="#id29" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>If you need to update your CUDA toolkit, you can visit the <a class="reference external" href="https://developer.nvidia.com/cuda-toolkit">NVIDIA website</a> (<a class="reference external" href="https://developer.nvidia.com/cuda-toolkit">https://developer.nvidia.com/cuda-toolkit</a>). Click on ‘NVIDIA CUDA Toolkit Download’ to access the latest version. Alternatively, if you require an earlier version, you can navigate to ‘Archive of Previous CUDA Releases’ on the NVIDIA website to find the specific CUDA toolkit version you need.</p>
<figure class="align-center" id="id30">
<a class="reference internal image-reference" href="_images/W23.png"><img alt="_images/W23.png" src="_images/W23.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">NVIDIA website to download CUDA toolkit</span><a class="headerlink" href="#id30" title="Link to this image"></a></p>
</figcaption>
</figure>
<figure class="align-center" id="id31">
<a class="reference internal image-reference" href="_images/W24.png"><img alt="_images/W24.png" src="_images/W24.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">NVIDIA CUDA toolkit download</span><a class="headerlink" href="#id31" title="Link to this image"></a></p>
</figcaption>
</figure>
<figure class="align-center" id="id32">
<a class="reference internal image-reference" href="_images/W25.png"><img alt="_images/W25.png" src="_images/W25.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">NVIDIA CUDA toolkit (Latest version)</span><a class="headerlink" href="#id32" title="Link to this image"></a></p>
</figcaption>
</figure>
<figure class="align-center" id="id33">
<a class="reference internal image-reference" href="_images/W26.png"><img alt="_images/W26.png" src="_images/W26.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">NVIDIA CUDA toolkit (Earlier versions)</span><a class="headerlink" href="#id33" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Follow the download and installation instructions provided on the NVIDIA website to update or install the CUDA toolkit on your Windows device. This ensures that Maxwell-TD and other CUDA-dependent applications can function correctly.</p>
</section>
<section id="windows-version">
<h3>Windows Version<a class="headerlink" href="#windows-version" title="Link to this heading"></a></h3>
<p>Make sure your Windows 10 or 11 system meets the following requirements:</p>
<ul class="simple">
<li><p><strong>WSL Version:</strong> Ensure WSL version 1.1.3.0 or newer.</p></li>
<li><p><strong>Windows 11:</strong> 64-bit Home or Pro version 21H2 or later, or Enterprise or Education version 21H2 or later.</p></li>
<li><p><strong>Windows 10:</strong> 64-bit Home or Pro version 22H2 (build 19045) or later, or Enterprise or Education version 22H2 (build 19045) or later. The minimum supported version is Home or Pro 21H2 (build 19044) or later, or Enterprise or Education 21H2 (build 19044) or later.</p></li>
</ul>
<div class="admonition note">
<p class="admonition-title">Note</p>
<ul class="simple">
<li><p>Docker Desktop on Windows is supported only on versions of Windows that are still actively serviced by Microsoft. It is not compatible with Windows Server versions like Windows Server 2019 or Windows Server 2022.</p></li>
<li><p>Containers and images created with Docker Desktop are shared across all user accounts on the same machine, as they use a common VM for building and running containers. However, sharing containers and images between user accounts is not supported when using the Docker Desktop WSL 2 backend.</p></li>
</ul>
</div>
</section>
<section id="sufficient-memory-to-upload-image">
<h3>Sufficient Memory to upload image<a class="headerlink" href="#sufficient-memory-to-upload-image" title="Link to this heading"></a></h3>
<p>Make sure your system has adequate storage space for the image. The current image requires 10GB for storage while zipped. Once extracted, it occupies an additional 10GB on your system, although it remains hidden from regular users. You can view these hidden images and containers using Docker Desktop.</p>
<figure class="align-center" id="id34">
<a class="reference internal image-reference" href="_images/W42.png"><img alt="_images/W42.png" src="_images/W42.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">View all containers or image on Docker Desktop</span><a class="headerlink" href="#id34" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>Users can remove any unwanted images or containers using the ‘delete’ button.</p>
<figure class="align-center" id="id35">
<a class="reference internal image-reference" href="_images/W43.png"><img alt="_images/W43.png" src="_images/W43.png" style="width: 1200px;" /></a>
<figcaption>
<p><span class="caption-text">Delete if not needed to free up space</span><a class="headerlink" href="#id35" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>If necessary, resort to command-line operations to reclaim system resources. Execute these commands in a PowerShell console with administrative privileges.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Purging All Unused or Dangling Resources</span>
docker<span class="w"> </span>system<span class="w"> </span>prune
<span class="c1"># Remove stopped containers and all unused images</span>
docker<span class="w"> </span>system<span class="w"> </span>prune<span class="w"> </span>-a
<span class="c1"># Removing Docker Images</span>
<span class="c1">## Remove Specific Images</span>
<span class="c1"># List all images (including intermediate layers)</span>
docker<span class="w"> </span>images<span class="w"> </span>-a
<span class="c1"># Remove specific image(s) using their ID or tag</span>
docker<span class="w"> </span>rmi<span class="w"> </span>&lt;image_id_or_name&gt;
<span class="c1">## Remove Dangling Images</span>
<span class="c1"># List dangling images</span>
docker<span class="w"> </span>images<span class="w"> </span>-f<span class="w"> </span><span class="nv">dangling</span><span class="o">=</span><span class="nb">true</span>
<span class="c1"># Remove dangling images</span>
docker<span class="w"> </span>image<span class="w"> </span>prune
<span class="c1">## Remove Images Matching a Pattern</span>
<span class="c1"># List images matching a pattern (using grep)</span>
docker<span class="w"> </span>images<span class="w"> </span>-a<span class="w"> </span><span class="p">|</span><span class="w"> </span>grep<span class="w"> </span><span class="s2">&quot;pattern&quot;</span>
<span class="c1"># Remove images matching a pattern using awk and xargs</span>
docker<span class="w"> </span>images<span class="w"> </span>-a<span class="w"> </span><span class="p">|</span><span class="w"> </span>grep<span class="w"> </span><span class="s2">&quot;pattern&quot;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>awk<span class="w"> </span><span class="s1">&#39;{print $1&quot;:&quot;$2}&#39;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>xargs<span class="w"> </span>docker<span class="w"> </span>rmi
<span class="c1">## Remove All Images</span>
<span class="c1"># Remove all Docker images</span>
docker<span class="w"> </span>rmi<span class="w"> </span><span class="k">$(</span>docker<span class="w"> </span>images<span class="w"> </span>-a<span class="w"> </span>-q<span class="k">)</span>
<span class="c1"># Removing Containers</span>
<span class="c1">## Remove Specific Containers</span>
<span class="c1"># List all containers (including stopped ones)</span>
docker<span class="w"> </span>ps<span class="w"> </span>-a
<span class="c1"># Remove specific container(s)</span>
docker<span class="w"> </span>rm<span class="w"> </span>&lt;container_id_or_name&gt;
<span class="c1">## Remove All Exited Containers</span>
<span class="c1"># List all exited containers</span>
docker<span class="w"> </span>ps<span class="w"> </span>-a<span class="w"> </span>-f<span class="w"> </span><span class="nv">status</span><span class="o">=</span>exited
<span class="c1"># Remove all exited containers</span>
docker<span class="w"> </span>rm<span class="w"> </span><span class="k">$(</span>docker<span class="w"> </span>ps<span class="w"> </span>-a<span class="w"> </span>-f<span class="w"> </span><span class="nv">status</span><span class="o">=</span>exited<span class="w"> </span>-q<span class="k">)</span>
<span class="c1">## Remove Containers Matching a Pattern</span>
<span class="c1"># List containers matching a pattern (using grep)</span>
docker<span class="w"> </span>ps<span class="w"> </span>-a<span class="w"> </span><span class="p">|</span><span class="w"> </span>grep<span class="w"> </span><span class="s2">&quot;pattern&quot;</span>
<span class="c1"># Remove containers matching a pattern using awk and xargs</span>
docker<span class="w"> </span>ps<span class="w"> </span>-a<span class="w"> </span><span class="p">|</span><span class="w"> </span>grep<span class="w"> </span><span class="s2">&quot;pattern&quot;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>awk<span class="w"> </span><span class="s1">&#39;{print $1}&#39;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>xargs<span class="w"> </span>docker<span class="w"> </span>rm
<span class="c1">## Stop and Remove All Containers</span>
<span class="c1"># Stop all containers</span>
docker<span class="w"> </span>stop<span class="w"> </span><span class="k">$(</span>docker<span class="w"> </span>ps<span class="w"> </span>-a<span class="w"> </span>-q<span class="k">)</span>
<span class="c1"># Remove all containers</span>
docker<span class="w"> </span>rm<span class="w"> </span><span class="k">$(</span>docker<span class="w"> </span>ps<span class="w"> </span>-a<span class="w"> </span>-q<span class="k">)</span>
</pre></div>
</div>
</section>
<section id="bios-settings">
<h3>BIOS settings<a class="headerlink" href="#bios-settings" title="Link to this heading"></a></h3>
<p>To enable Docker server virtualization on Windows, it’s crucial to ensure that virtualization is enabled in your computer’s BIOS settings. This setting can only be modified by restarting your machine and accessing the BIOS configuration. Virtualization support in BIOS allows Windows to utilize Docker server features effectively. It’s a necessary step to ensure Docker containers run efficiently on your system.</p>
</section>
<section id="change-simulation-parameters">
<h3>Change Simulation Parameters<a class="headerlink" href="#change-simulation-parameters" title="Link to this heading"></a></h3>
<p>To modify simulation parameters, you can edit the <code class="docutils literal notranslate"><span class="pre">CUDA_LTS_RUN.sh</span></code> shell script. This script contains flags or variables that control various aspects of the DGTD simulation. The script includes comments or descriptions to explain the variables’ or flags’ purpose.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;===========&quot;</span>
<span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;EXECUTABLE&quot;</span>
<span class="nv">EXE</span><span class="o">=</span><span class="s2">&quot;./maxwelltd_CUDA_LTS_DOUBLEpre_FLOATpro&quot;</span>
<span class="nb">echo</span><span class="w"> </span><span class="nv">$EXE</span>
<span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;FileName&quot;</span>
<span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;===========&quot;</span>
<span class="c1"># 0. [EXE]</span>
<span class="c1"># 1. Filename: Simulation Filename</span>
<span class="c1"># 2. Freq: Central Modulation Frequency (MHz)</span>
<span class="c1"># 3. Planewave Waveform (Excitation Type): (0)Time Harmonic (1)Gauss (2)Neumann (3) Modulated Gauss;</span>
<span class="c1"># 4. Port Waveform (0) Time Harmonic Pulse (1) Gaussian Pulse</span>
<span class="c1"># 5. Tdelay: Delay of excitation pulse (sec)</span>
<span class="c1"># 6. Tau: Width of pulse (sec)</span>
<span class="c1"># 7. FinalTime: Termination Time (sec)</span>
<span class="c1"># 8. Gamma (Penalty) --&gt; 1 upwind , 0 central</span>
<span class="c1"># 9. VTU --&gt; 0 (YES), 1 (NO)</span>
<span class="c1">#10. Surface Field Output BC Surfaces --&gt; (0) Off (1) PEC only (2) FieldPlane only (3) FieldPlane and PEC</span>
<span class="c1">#11. Surface Output Types --&gt; (0) Field (1) Current (2) Field and Current</span>
<span class="c1">#12. Poly order --&gt; (1) First Order (2) Second Order</span>
<span class="c1">#13. Free Space Comparison(Analytical): (0) True and (1) False</span>
<span class="c1">#14. SAMPLINGRATE : parameter of Pade approximation</span>
<span class="c1">#15. PADE : (0) Pade mode is Off (2) Pade mode is on</span>
<span class="nv">FILENAME</span><span class="o">=</span>cylinder_cr1.75
<span class="nv">FREQ</span><span class="o">=</span><span class="m">2650</span>
<span class="nv">PLANEWAVEFLAG</span><span class="o">=</span><span class="m">1</span>
<span class="nv">PORTFLAG</span><span class="o">=</span><span class="m">1</span>
<span class="nv">TD</span><span class="o">=</span><span class="m">2</span>.5e-9
<span class="nv">TAU</span><span class="o">=</span><span class="m">2</span>.5e-10
<span class="nv">FINALTIME</span><span class="o">=</span>25e-8
<span class="nv">GAMMA</span><span class="o">=</span><span class="m">0</span>.025
<span class="nv">VTU</span><span class="o">=</span><span class="m">1</span>
<span class="nv">SURFFIELDOUTBCSURFS</span><span class="o">=</span><span class="m">0</span>
<span class="nv">SURFOUTTYPES</span><span class="o">=</span><span class="m">0</span>
<span class="nv">POLYORDER</span><span class="o">=</span><span class="m">2</span>
<span class="nv">ANALYTICAL</span><span class="o">=</span><span class="m">1</span>
<span class="nv">SAMPLINGRATE</span><span class="o">=</span><span class="m">12</span>.5
<span class="nv">PADE</span><span class="o">=</span><span class="m">2</span>
rm<span class="w"> </span>*.log
rm<span class="w"> </span>*.vtu
rm<span class="w"> </span>AnalyticalIncidentField*
rm<span class="w"> </span>Probes_*
rm<span class="w"> </span>*.TD*
rm<span class="w"> </span>-r<span class="w"> </span>./TimeDomainVoltages
<span class="nv">$EXE</span><span class="w"> </span><span class="nv">$FILENAME</span><span class="w"> </span><span class="nv">$FREQ</span><span class="w"> </span><span class="nv">$PLANEWAVEFLAG</span><span class="w"> </span><span class="nv">$PORTFLAG</span><span class="w"> </span><span class="nv">$TD</span><span class="w"> </span><span class="nv">$TAU</span><span class="w"> </span><span class="nv">$FINALTIME</span><span class="w"> </span><span class="nv">$GAMMA</span><span class="w"> </span><span class="nv">$VTU</span><span class="w"> </span><span class="nv">$SURFFIELDOUTBCSURFS</span><span class="w"> </span><span class="nv">$SURFOUTTYPES</span><span class="w"> </span><span class="nv">$POLYORDER</span><span class="w"> </span><span class="nv">$ANALYTICAL</span><span class="w"> </span><span class="nv">$SAMPLINGRATE</span><span class="w"> </span><span class="nv">$PADE</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>tee<span class="w"> </span>-a<span class="w"> </span>compute.log
rm<span class="w"> </span>-r<span class="w"> </span>./VTU_LTS
mkdir<span class="w"> </span>./VTU_LTS
mv<span class="w"> </span>*.vtu<span class="w"> </span>./VTU_LTS
rm<span class="w"> </span>-r<span class="w"> </span>./PROBES
mkdir<span class="w"> </span>./PROBES
mv<span class="w"> </span>*.csv<span class="w"> </span>./PROBES
mv<span class="w"> </span>*.TD*<span class="w"> </span>./PROBES
mv<span class="w"> </span>*.log<span class="w"> </span>./PROBES
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