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<h1 id="hpc-guide">HPC Guide</h1>
<p>Full documentation: <a href="https://docs.hpc.ugent.be/">https://docs.hpc.ugent.be/</a></p>
<h2 id="storage-overview">Storage Overview</h2>
<ul>
<li><strong>Run Outputs</strong>: Written to <code>$VSC_SCRATCH</code> during the job (fast I/O) and copied to <code>$VSC_DATA</code> at the end for persistence.</li>
<li><strong>Virtual Environments</strong>: Managed on <strong><code>$VSC_DATA</code></strong> by mirroring configuration files. This avoids the 3GB home quota without requiring symlinks in the project root.</li>
</ul>
<h2 id="initial-environment-setup">Initial Environment Setup</h2>
<p>Run <strong>once</strong> after cloning the repository. This script handles all modules, mirroring, and environment synchronization.</p>
<div class="highlight"><pre><span></span><code><span class="c1"># Option A: Interactive (on a compute node)</span>
module<span class="w"> </span>swap<span class="w"> </span>cluster/donphan<span class="w">  </span><span class="c1"># Debug cluster (CPU only)</span>
<span class="c1"># OR for GPU clusters:</span>
<span class="c1"># module swap cluster/joltik</span>
<span class="c1"># module swap cluster/accelgor</span>
<span class="c1"># module swap cluster/litleo</span>

qsub<span class="w"> </span>-I<span class="w"> </span>-l<span class="w"> </span><span class="nv">nodes</span><span class="o">=</span><span class="m">1</span>:gpus<span class="o">=</span><span class="m">1</span><span class="w">  </span><span class="c1"># Only for GPU clusters</span>
<span class="nb">cd</span><span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">PBS_O_WORKDIR</span><span class="si">}</span><span class="s2">&quot;</span>
bash<span class="w"> </span>scripts/hpc/install.sh

<span class="c1"># Option B: Batch (Run in background)</span>
<span class="c1"># NOTE: GPU clusters (joltik/accelgor/litleo) require -l gpus=1 at runtime</span>
qsub<span class="w"> </span>-l<span class="w"> </span><span class="nv">gpus</span><span class="o">=</span><span class="m">1</span><span class="w"> </span>scripts/hpc/install.sh
</code></pre></div>
<h2 id="production-vs-debug-clusters">Production vs. Debug Clusters</h2>
<p>Our scripts are cluster-agnostic and do <strong>not</strong> have hardcoded GPU requirements. Instead, you must request GPUs at runtime using the <code>-l gpus=1</code> flag when submitting to a production GPU cluster.</p>
<h3 id="debugging-donphan">Debugging (Donphan)</h3>
<p>The <code>donphan</code> cluster does not support GPUs. Simply run the scripts without extra resource flags:
<div class="highlight"><pre><span></span><code>module<span class="w"> </span>swap<span class="w"> </span>cluster/donphan
qsub<span class="w"> </span>scripts/hpc/train.pbs
</code></pre></div></p>
<h3 id="production-joltik-accelgor-litleo">Production (Joltik, Accelgor, Litleo)</h3>
<p>These clusters provide GPU acceleration and <strong>require</strong> a GPU request at runtime:
<div class="highlight"><pre><span></span><code>module<span class="w"> </span>swap<span class="w"> </span>cluster/joltik<span class="w">  </span><span class="c1"># or accelgor/litleo</span>
qsub<span class="w"> </span>-l<span class="w"> </span><span class="nv">gpus</span><span class="o">=</span><span class="m">1</span><span class="w"> </span>scripts/hpc/train.pbs
</code></pre></div></p>
<h2 id="interactive-debugging">Interactive Debugging</h2>
<p>To activate your environment for interactive work, simply run the same <code>install.sh</code> script.</p>
<div class="highlight"><pre><span></span><code>qsub<span class="w"> </span>-I<span class="w"> </span>-l<span class="w"> </span><span class="nv">nodes</span><span class="o">=</span><span class="m">1</span>:ppn<span class="o">=</span><span class="m">4</span><span class="w"> </span>-l<span class="w"> </span><span class="nv">walltime</span><span class="o">=</span><span class="m">1</span>:00:00
<span class="nb">cd</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$PBS_O_WORKDIR</span><span class="s2">&quot;</span>
bash<span class="w"> </span>scripts/hpc/install.sh
</code></pre></div>
<h3 id="verification-commands">Verification Commands</h3>
<p>After installation, run these commands to ensure your environment is set up correctly:</p>
<ol>
<li>
<p><strong>Verify Quota Safety</strong>:
   <div class="highlight"><pre><span></span><code>ls<span class="w"> </span>-d<span class="w"> </span>venvs<span class="w"> </span><span class="m">2</span>&gt;/dev/null<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;FAIL&quot;</span><span class="w"> </span><span class="o">||</span><span class="w"> </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;&gt;&gt;&gt; PASS: Project root is clean.&quot;</span>
</code></pre></div></p>
</li>
<li>
<p><strong>Verify Library Versions (NumPy Fix)</strong>:
   <div class="highlight"><pre><span></span><code>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">&quot;import numpy; print(f&#39;NumPy: {numpy.__version__}&#39;)&quot;</span>
<span class="c1"># Expected: 2.x.x (Venv version), not 1.2x (System version)</span>
</code></pre></div></p>
</li>
<li>
<p><strong>Verify GPU Access</strong>:
   <div class="highlight"><pre><span></span><code>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">&quot;import torch, jax; print(f&#39;GPU: {torch.cuda.is_available()}&#39;); print(f&#39;JAX: {jax.devices()}&#39;)&quot;</span>
</code></pre></div></p>
</li>
</ol>
<h2 id="managing-dependencies">Managing Dependencies</h2>
<p><code>env/hpc/requirements.txt</code> is auto-generated from <code>pyproject.toml</code>. To regenerate:</p>
<div class="highlight"><pre><span></span><code>uv<span class="w"> </span>run<span class="w"> </span>scripts/hpc/export_requirements.py
</code></pre></div>
<p>Modules listed in <code>env/hpc/modules.txt</code> are automatically excluded from the pip requirements to save space and use HPC-optimized binaries.</p>


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