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    "title": "Legal Information",
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    "body": "<div class=\"component__inner text__inner\"><div class=\"component__header text__header\" id=\"65faaa76c8c979040898fffe-header\"><div class=\"component__header-inner text__header-inner\"><div class=\"component__body text__body\"><div class=\"component__body-inner text__body-inner\"><p>The E-learning training presented here is part of the&nbsp;<strong><a href=\"https://portal.hpc.hsu-hh.de/\">HPC Portal</a></strong>, developed within the&nbsp;<strong><a href=\"https://dtecbw.de/home\">dtec.bw</a></strong>-funded project <strong><a href=\"http://www.hsu-hh.de/hpccp/project-description/\">hpc.bw</a>.</strong> The content has been created collaboratively by the <strong><a href=\"https://www.hsu-hh.de/wb/\">Chair of Continuing Education/Lifelong Learning</a></strong> and the <strong><a href=\"https://www.hsu-hh.de/hpc/\">Chair of High Performance Computing</a></strong>.</p><p>While the training materials are developed with great care and to the best of our knowledge, they do not claim to be exhaustive or free from error. As the content is not continously updated, it may not always reflect the latest developments. The training is not part of a formal curriculum and does not provide certification; rather, it is intended to support individual learning.&nbsp;</p><p>This training material has been created using the <a href=\"https://www.adaptlearning.org\"><strong>Adapt Authoring Tool</strong></a> and is published as Open Educational Resource (OER) under a <a href=\"https://creativecommons.org/licenses/by/4.0/\"><strong>CC BY</strong>&nbsp;<strong>4.0</strong></a> license. The source files for this training can be downloaded from the <strong><a href=\"https://portal.hpc.hsu-hh.de/training/hpc_workshop_1/\">respective information page</a></strong> on the <strong><a href=\"https://portal.hpc.hsu-hh.de\">HPC Portal</a></strong>.&nbsp;</p></div></div></div></div></div>",
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    "title": "Data Transfer via SCP",
    "displayTitle": "Data Transfer via SCP",
    "body": "<p><strong>1. Setting up your Terminal</strong></p><ul><li><strong>Linux or Mac Users</strong>: You dont need any special tools. Your default terminal should work perfectly.</li><li><strong>Windows Users</strong>: We recommend using <strong>PowerShell</strong> or downloading the <strong>Windows Terminal</strong> from the Microsoft Store. Both provide a user-friendly and reliable environment for this task.</li></ul><p><strong>2. Sending Files to HSUper</strong></p><p>When you want to <strong>upload </strong>a file from your local machine to the HSUper system, follow these steps:</p><p>&nbsp;&nbsp;&nbsp;&nbsp; a) <strong>Open Your Terminal</strong> and execute the following command:<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <span style=\"color:#000000\"><strong><span style=\"background-color:#ecf0f1\">scp</span></strong><em><strong><span style=\"background-color:#ecf0f1\"> </span></strong><span style=\"background-color:#ecf0f1\">&lt;filename&gt; &lt;user&gt;</span></em><strong><span style=\"background-color:#ecf0f1\">@hsuper-login01.hsu-hh.de</span></strong><em><span style=\"background-color:#ecf0f1\">:~/&lt;path&gt;</span></em></span><em><span style=\"background-color:#ecf0f1\">/</span></em></p><ul><li>Replace <em><span style=\"background-color:#ecf0f1\">&lt;filename&gt;</span> </em>with the name of the file you want to upload. If the file isn't in your current working directory, include its full path.</li><li><em><span style=\"background-color:#ecf0f1\">&lt;user&gt;</span></em> should be replaced with your HSUper username.</li><li>The part after the colon <em><span style=\"background-color:#ecf0f1\">(:~/&lt;path&gt;/)</span></em> specifies where the file will go on the HSUper system:<ul><li><em><span style=\"background-color:#ecf0f1\">~</span></em> points to your home folder on HSUper.</li><li><em><span style=\"background-color:#ecf0f1\">&lt;path</span></em>&gt; is the directory you want to copy the file to. If you’re unsure, navigate to the folder on HSUper where you want to place the file and note its path.</li></ul></li></ul><p><span style=\"color:#b90444\"><strong>Example:</strong></span> If your file is report.pdf and your HSUper username is student1, the command might look like this:</p><p><strong><span style=\"background-color:#ecf0f1\">scp report.pdf student1@hsuper-login01.hsu-hh.de:~/documents/</span></strong></p><p>&nbsp;&nbsp;&nbsp;&nbsp; b) Make sure you're either in the directory containing your file or include its full path in <em>&lt;filename&gt;</em>.</p><p>&nbsp;&nbsp;&nbsp;&nbsp; c) Remember, the <strong><span style=\"background-color:#ecf0f1\">:</span></strong> separates the HSUper hostname <strong><span style=\"background-color:#ecf0f1\">(hsuper-login01.hsu-hh.de</span></strong>) from the target path.</p><p><strong>3. Retrieving Files from HSUper</strong></p><p>If you need to <strong>download </strong>files from HSUper, you can follow these steps:</p><p>&nbsp;&nbsp;&nbsp;&nbsp; a) Use the following command in your terminal:<br />&nbsp;&nbsp;&nbsp;&nbsp; <span style=\"background-color:#ecf0f1\"><strong>scp<em> </em></strong><em>&lt;user&gt;</em><strong>@hsuper-login01.hsu-hh.de</strong><em>:~/&lt;path/filename&gt; .</em></span></p><ul><li>Replace <em><span style=\"background-color:#ecf0f1\">&lt;user&gt;</span></em> with your HSUper username.</li><li>Replace <em><span style=\"background-color:#ecf0f1\">~/&lt;path/filename&gt;</span></em> with the full path to the file you want to retrieve from HSUper. If you're unsure about the path, use the <strong><span style=\"background-color:#ecf0f1\">pwd</span></strong> command on HSUper to find and copy it.</li><li>The<span style=\"background-color:#ecf0f1\"> <strong>. </strong></span>at the end tells SCP to save the file in your current working directory. Navigate to your desired folder first or specify a full path instead of <strong><span style=\"background-color:#ecf0f1\">.</span></strong>.</li></ul><p><span style=\"color:#b90444\"><strong>► Example:</strong></span> To download a file named <strong><span style=\"background-color:#ecf0f1\">data.csv</span></strong> located in the <strong><span style=\"background-color:#ecf0f1\">~/projects/</span></strong> directory on HSUper, the command would be:</p><p><strong><span style=\"background-color:#ecf0f1\">scp student1@hsuper-login01.hsu-hh.de:~/projects/data.csv .</span></strong></p><p><strong>4. </strong> <strong>SCP Syntax Overview</strong></p><p>You might notice that the SCP command looks a lot like the <strong><span style=\"background-color:#ecf0f1\">cp</span> </strong>command used for copying files locally. That’s because they share a similar syntax. Essentially, you’re specifying a source and a target:</p><p><span style=\"background-color:#ecf0f1\"><strong>scp</strong><em><strong> </strong>&lt;source&gt; &lt;target&gt;</em></span></p><p>Here, the source can be either your local machine or HSUper, and the target can be the other system.</p><p>&nbsp;</p><p>&nbsp;</p>",
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    "title": "Congratulations!",
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    "body": "<p>By following these steps, you’ll be able to transfer files quickly and securely between your local computer and HSUper.</p><p>On the next chapter you will learn about Data Transfer made simple via GUI Alternatives.</p><p>&nbsp;</p>",
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    "title": "Prerequisities",
    "displayTitle": "Prerequisities",
    "body": "<p>Before you begin, there are a two basic prerequisites you need to meet to ensure a useful experience.</p><p><strong>&nbsp;&nbsp;&nbsp;&nbsp; ✅ HSU network</strong></p><p>You need to be on a PC or laptop that is connected to the <strong>HSU network</strong>. This connection is crucial because it ensures that you have the appropriate <strong>network permissions</strong> to interact with HSUper.</p><p><strong>&nbsp;&nbsp;&nbsp;&nbsp; ✅ Access to HSUper</strong></p><p>Make sure that you have <strong>applied </strong>for and received the necessary <strong>access rights</strong> to HSUper. This is essential for accessing the system and its features. You can read the content of the training without having access but you will not be able to work on the tasks. Please apply for HSUper access using this <strong><a href=\"https://tickets.hsu-hh.de/kix/customer.pl?Action=CustomerTicketMessage;DefaultSet=149\" target=\"_blank\">form</a></strong> if needed.</p><p><strong>&nbsp;&nbsp;&nbsp;&nbsp; ✅ Completed the first training</strong></p><p>While none of the trainings are actually consecutive, it may be helpful to have completed the first and second training:</p><ul><li><a href=\"https://portal.hpc.hsu-hh.de/training/hpc_workshop_1/\"><strong>HPC Workshop 1 - A short introduction to HSUper and the LINUX Termina</strong>l</a></li></ul><p>You decide, whether you need that introduction before working your way through this training.</p><p>If you experience a challenge, you might want to have a look at the <strong><a href=\"https://portal.hpc.hsu-hh.de/documentation/hsuper/\" target=\"_blank\">HSUper documentation</a></strong> at the <strong><a href=\"https://portal.hpc.hsu-hh.de/\" target=\"_blank\">HPC Portal</a></strong>.</p><p>&nbsp;</p>",
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    "title": "WinSCP: A Windows-Friendly Solution",
    "displayTitle": "WinSCP: A Windows-Friendly Solution",
    "body": "<p>For Windows users, <strong>WinSCP</strong> is a fantastic tool for transferring files to and from your HPC system. Here’s why it’s so popular:</p><ul><li><strong>Drag-and-Drop Functionality:</strong> Simply drag files from your local machine to the remote cluster—or vice versa.</li><li><strong>Convenient File Management:</strong> You can create folders, rename files, and organize your data directly within the tool.</li></ul><p><strong>How to Use WinSCP:</strong></p><ol><li>Download and install WinSCP.</li><li>Connect to the cluster by entering the hostname, username, and password.</li><li>Use the dual-pane interface to drag and drop files between your local system and the cluster.</li></ol>",
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    "title": "Downloading Files with wget",
    "displayTitle": "Downloading Files with wget",
    "body": "<p>Sometimes you need to download a single file from a web address. The <strong>wget</strong> command makes this straightforward.</p><p><span style=\"color:#b90444\"><strong>Example:</strong></span> To download the HSU logo, use:</p><p><strong><span style=\"background-color:#dddddd\">wget https://www.hsu-hh.de/wp-content/themes/hsu/img/hsulogo.png</span></strong></p><p>What happens next?</p><ul><li><strong><span style=\"background-color:#dddddd\">wget</span> </strong>fetches the file from the URL and saves it to your current working directory.</li></ul><p><strong><span style=\"color:#b90444\">Pro Tip</span>:</strong> This command is great for downloading files directly to remote systems where using a browser isn’t practical.</p>",
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    "instruction": "Compare this with your output.",
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    "title": "Conclusion",
    "displayTitle": "Conclusion",
    "body": "<p>By understanding HSUper’s hardware setup&nbsp;— <strong>72 CPU</strong> <strong>cores </strong>and <strong>256 GB of RAM</strong> per node — you can better plan your jobs to take full advantage of the available resources.</p>",
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    "title": "Conclusion",
    "displayTitle": "Conclusion",
    "body": "<p>With <strong><span style=\"background-color:#ecf0f1\">htop</span></strong>, you can gain valuable insights into system utilization, whether on the login node or a compute node during a job. This helps you make smarter decisions about resource allocation, debug jobs in real time, and optimize your workflows.</p>",
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    "title": "Linux Alternative: GNOME’s File Manager",
    "displayTitle": "Linux Alternative: GNOME’s File Manager",
    "body": "<p>If you’re on Linux and use the GNOME desktop environment, you already have a built-in solution for remote file management:</p><ul><li>Open your file manager and go to <strong>Files → Connect to Server</strong>.</li><li>Enter the cluster’s connection details, and your remote files will appear as if they’re part of your local file system.</li><li>This option is intuitive and integrates seamlessly into your workflow.</li></ul>",
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    "title": "Cross-Platform Option: FileZilla",
    "displayTitle": "Cross-Platform Option: FileZilla",
    "body": "<p>Another excellent alternative is <strong>FileZilla</strong>, a cross-platform FTP client that supports SSH file transfer:</p><ul><li><strong>Why FileZilla?</strong> It combines a graphical interface with advanced options for those who want more control.</li><li>Like WinSCP, FileZilla supports drag-and-drop transfers, and it’s available for Windows, Linux, and macOS.</li></ul><p><strong>Getting Started with FileZilla:</strong></p><ol><li>Download and install FileZilla.</li><li>Configure the connection by entering the cluster's hostname, username, and password.</li><li>Start transferring files with its straightforward interface.</li></ol>",
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    "title": "Cloning Repositories with Git",
    "displayTitle": "Cloning Repositories with Git",
    "body": "<p>Do you need to download code or resources from an online repository? <strong>Git</strong> is the perfect tool for this.</p><p><span style=\"color:#b90444\"><strong>Example:</strong></span> To clone a repository, run the following command:</p><p><strong><span style=\"background-color:#ecf0f1\">git clone https://github.com/HSU-HPC/MaMiCo.git</span></strong></p><p>Here’s what happens:</p><ul><li>The command downloads all files from the specified repository into a new folder named MaMiCo.</li><li>You can now navigate to this folder and start working with the code.</li></ul><p>Git is widely used in software development but is equally valuable for managing and distributing research scripts or datasets stored in repositories.</p>",
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    "title": "Mounting Remote Locations with sshfs",
    "displayTitle": "Mounting Remote Locations with sshfs",
    "body": "<p>If you’re an advanced user working on Linux or macOS, <strong>sshfs</strong> lets you mount a remote directory (like HSUper) on your local machine as if it were part of your local filesystem.</p><p><strong>Key Benefits:</strong></p><ul><li>Access and edit remote files directly without downloading them.</li><li>Simplify workflows for certain development or data analysis tasks.</li></ul><p><span style=\"color:#b90444\"><strong>Cautions:</strong></span></p><ul><li>Only use <strong>sshfs</strong> in stable network conditions. Avoid using it on Wi-Fi or laptops that move between networks frequently — it works best in stationary setups.</li></ul><p><span style=\"color:#b90444\"><strong>Example Use Case:</strong></span> Mount a directory on HSUper with:</p><p><strong><span style=\"background-color:#dddddd\">sshfs &lt;user&gt;@hsuper-login01.hsu-hh.de:~/&lt;path&gt; &lt;local-mount-point&gt;</span></strong></p><p>&nbsp;</p>",
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    "title": "An Alternative to sshfs: rclone",
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    "body": "<p>For users seeking flexibility across platforms, <strong>rclone</strong> is a great alternative. It works on Windows, macOS, and Linux.</p><p><strong>What is rclone?</strong></p><ul><li>A command-line tool for managing and syncing files between your local system and various cloud or remote storage locations, including HPC clusters.</li></ul><p><strong>Why Choose rclone?</strong></p><ul><li>It offers robust options for syncing large datasets or managing remote files with minimal hassle.</li><li>Unlike sshfs, it’s less sensitive to unstable networks.</li></ul>",
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    "title": "Conclusion",
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    "body": "<p>These command-line tools provide advanced options for transferring and managing data. Here’s a quick summary:</p><ul><li><strong>Git:</strong> Clone repositories for collaborative projects.</li><li><strong>wget:</strong> Download individual files via a URL.</li><li><strong>sshfs:</strong> Mount remote directories for direct file access (Linux/macOS only).</li><li><strong>rclone:</strong> A flexible, cross-platform alternative for syncing files.</li></ul><p>Choose the tool that best fits your needs, whether you’re retrieving code, downloading files, or working directly with remote directories. In our next session, we’ll cover strategies for automating data transfers and backups.</p>",
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    "body": "<p>The HPC system uses specific file paths to organize storage and software. Understanding these paths will make it easier to navigate and manage your files.</p>",
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        "title": "$HOME",
        "body": "<p>Your personal home directory, where your files and settings are stored.</p><p><br /><strong><span style=\"color:#b90444\">Example:</span> <span style=\"background-color:#ecf0f1\">/beegfs/home/j/jarmatzp</span></strong></p>",
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    "body": "<p><strong>Minimize the Number of Files:</strong><br />Instead of creating many small files, consolidate data into fewer large files whenever possible. This improves performance and reduces the overhead on the file system. For example, consider using formats like <strong>HDF5</strong> for storing large datasets.</p>",
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    "title": "Conclusion",
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    "body": "<p>By understanding file quotas and key system paths, you’ll navigate your HPC environment with ease and ensure efficient data management. Always monitor your quota with <strong><span style=\"background-color:#ecf0f1\">beegfs-quota</span></strong>, familiarize yourself with important directories like <strong><span style=\"background-color:#ecf0f1\">$HOME</span></strong> and <strong><span style=\"background-color:#ecf0f1\">$SCRATCH</span></strong>, and follow best practices for file organization.</p><p>In the next chapter, we’ll explore how to get information about the <strong>HSUper Hardware Resources.</strong></p>",
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    "body": "<p>All <strong>compute nodes</strong> and the <strong>login node</strong> are equipped with the same hardware. This ensures predictable performance, so you can test on the login node and expect similar results on the compute nodes during execution.</p><p>To learn more about the processors in HSUper, use these <strong>commands</strong>:</p><p><strong><span style=\"background-color:#ecf0f1\">cat /proc/cpuinfo</span></strong></p><p>or</p><p><strong><span style=\"background-color:#ecf0f1\">lscpu</span></strong></p>",
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    "title": "Meet htop: A Terminal-Based Task Manager",
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    "body": "<p>To get a live overview of running processes and resource usage, the tool <strong><span style=\"background-color:#ecf0f1\">htop</span></strong> is your go-to solution. It provides a user-friendly, color-coded display right in the terminal.</p><p><strong>Key Features of htop:</strong></p><ul><li>View all running processes on the node.</li><li>Monitor <strong>CPU usage</strong>, <strong>RAM consumption</strong>, and the load on the system.</li><li>Sort processes by resource usage to identify heavy tasks.</li></ul>",
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    "body": "<p>HSUper utilizes the open-source workload manager <strong>Slurm</strong> to handle job scheduling and cluster management.</p><p><span style=\"color:#bf2d65\"><strong>Quick Tips About Slurm:</strong></span></p><ul><li>All Slurm commands start with the letter <strong><span style=\"background-color:#ecf0f1\">s</span></strong>, making them easy to remember.</li><li>You can use Slurm commands to check cluster status, inspect job details, and manage your workflows.</li></ul>",
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    "title": "Conclusion",
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    "body": "<p>With Slurm, you have a suite of tools to monitor and manage the cluster effectively:</p><ul><li>Use <strong><span style=\"background-color:#ecf0f1\">sinfo -s</span></strong> to check the status of partitions and nodes.</li><li>Use <strong><span style=\"background-color:#ecf0f1\">scontrol show</span></strong><span style=\"background-color:#ecf0f1\"> </span>for detailed information about specific entities.</li><li>Use <strong><span style=\"background-color:#ecf0f1\">squeue</span></strong> or <strong><span style=\"background-color:#ecf0f1\">squeue --me</span></strong> to track the job queue and your own tasks.</li></ul><p>In the next session, we’ll explore how to submit and configure jobs using Slurm. See you then!</p>",
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    "body": "<ul><li><p><strong>On the Login Node:</strong><br />Use <strong><span style=\"background-color:#dddddd\">htop</span></strong> to check how busy the login node is. This is particularly useful if you’re compiling or installing software and need to decide how many threads you can safely use without overloading the system.</p><p><strong>Example Question to Answer:</strong><br />“Can I use 8 threads to compile my code, or is the login node already at its limit?”</p></li><li><p><strong>On a Compute Node During a Job:</strong><br />If you’re running a job, you can SSH into the corresponding compute node and use htop to see how it’s performing.</p><p><strong>Example Insights:</strong></p><ul><li>Is your job utilizing all allocated cores effectively?</li><li>Is <strong>hyper-threading</strong> enabled or disabled on the node?</li></ul></li></ul>",
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    "body": "<p>Use the following commands to understand the state of the cluster:</p><ul><li><p><strong><span style=\"background-color:#ecf0f1\">sinfo -s</span>:</strong><br />This command provides a summary of the cluster's partitions and node utilization.</p><p><strong>What You’ll See:</strong></p><ul><li>A breakdown of node states using the labels <strong>A/I/O/T</strong>, which stand for:<ul><li><strong>A</strong>: Allocated (nodes currently in use)</li><li><strong>I</strong>: Idle (nodes available for jobs)</li><li><strong>O</strong>: Other (nodes in other states, such as down or drained)</li><li><strong>T</strong>: Total (total number of nodes in the partition)</li></ul></li></ul><p>This is a great way to quickly gauge how busy the cluster is.</p></li><li><p><strong><span style=\"background-color:#ecf0f1\">scontrol show</span>:</strong><br />Use this command to display detailed information about specific entities in the cluster, such as nodes, jobs, or partitions.</p></li><li><p><strong><span style=\"color:#bf2d65\">Example</span>:</strong></p><p><strong><span style=\"background-color:#ecf0f1\">scontrol show partition small</span></strong><br /><br />This will display detailed information about the partition named <strong><span style=\"background-color:#ecf0f1\">small</span></strong>.</p></li></ul>",
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    "body": "<p>To see which jobs are currently running or queued, use:</p><ul><li><p><strong><span style=\"background-color:#ecf0f1\">squeue</span>:</strong><br />Displays the current job queue of the entire cluster.</p></li><li><p><strong><span style=\"background-color:#ecf0f1\">squeue --me</span>:</strong><br />Displays only the jobs that you own, giving you a personalized view of your submitted tasks.</p></li></ul><p><span style=\"color:#bf2d65\"><strong>Pro Tip</strong></span><strong>:</strong> Use these commands regularly to track the status of your jobs and adjust your submissions if the cluster is busy.</p>",
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    "title": "Working on the tasks:",
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    "body": "<p><strong><span style=\"background-color:#ecf0f1\">git clone https://git.hpc.hsu-hh.de/cbrz/workshop-tasks.git</span></strong></p><ol><li>Do <strong>cd workshop-tasks</strong> to enter the workshop tasks.<br />&nbsp;</li><li>Use e.g. <strong><span style=\"background-color:#ecf0f1\">cd 1_beginner/2_HSUper/2_1</span></strong> to enter a task.<br />&nbsp;</li><li>Enter <strong><span style=\"background-color:#ecf0f1\">cat showtask.txt</span></strong> to see what you should do.<br />&nbsp;</li><li>Follow the instructions.<br />&nbsp;</li><li>Once you finished, use <strong><span style=\"background-color:#ecf0f1\">./check_solution</span></strong> to check if you succeeded</li></ol>",
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    "title": "Congratulations",
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    "body": "<p><span style=\"color:#b90444\"><strong>Congratulations!</strong></span></p><p>You successfully completed the the course <strong><span style=\"color:#b90444\">HPC Workshop 2 - Data Transfer and System Resources</span>&nbsp;</strong>and learned a lot about</p><ul><li>Data Transfer</li><li>System Resources</li></ul><p>We hope you had a good time with this training and the materials on the <strong><a href=\"https://portal.hpc.hsu-hh.de/\">HPC Portal</a></strong>.</p><p>Please let us know if you need support with anything.</p><p>Email: <strong><a href=\"mailto:hpc-portal@hsu-hh.de?subject=HPC%20Workshop%201%20-%20Support\">hpc-portal@hsu-hh.de</a></strong></p>",
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