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Allocation of nodes
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<h1 id="online-data-analysis">Online data analysis<a class="headerlink" href="#online-data-analysis" title="Permanent link">&para;</a></h1>
<p>We can access the online computing resources from the beamline consoles when logged in as the e-account.</p>
<h2 id="allocation-of-nodes">Allocation of nodes<a class="headerlink" href="#allocation-of-nodes" title="Permanent link">&para;</a></h2>
<p>Check available nodes and allocate one:</p>
<div class="highlight"><pre><span></span><code>sinfo
salloc<span class="w"> </span>-A<span class="w"> </span>csaxs<span class="w"> </span>-p<span class="w"> </span>csaxs<span class="w"> </span>-w<span class="w"> </span><span class="o">[</span>ra-c-110<span class="o">]</span>
ssh<span class="w"> </span>-Y<span class="w"> </span><span class="o">[</span>ra-c-110<span class="o">]</span>
</code></pre></div>
<p>Or for a GPU node:</p>
<div class="highlight"><pre><span></span><code>salloc<span class="w"> </span>-A<span class="w"> </span>csaxs<span class="w"> </span>-p<span class="w"> </span>gpu-csaxs<span class="w"> </span>--gpus<span class="o">=</span><span class="m">4</span><span class="w"> </span><span class="o">[</span>-w<span class="w"> </span>ra-gpu-003<span class="o">]</span><span class="w"> </span>--mem<span class="o">=</span>100G<span class="w"> </span>-n<span class="w"> </span><span class="m">8</span>
ssh<span class="w"> </span>-Y<span class="w"> </span><span class="o">[</span>ra-gpu-003<span class="o">]</span>
</code></pre></div>
<p>(note that we need to ask them to explicitly use one of our GPU nodes there, and this needs a couple of days to set up)</p>
<h3 id="specifications-of-the-computing-nodes">Specifications of the computing nodes<a class="headerlink" href="#specifications-of-the-computing-nodes" title="Permanent link">&para;</a></h3>
<p>A few examples of the available nodes:</p>
<table>
<thead>
<tr>
<th>Node</th>
<th>CPU</th>
<th>Cores</th>
<th>Memory</th>
<th>GPUs</th>
<th>Partition</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>ra-c-110</code></td>
<td>Intel Xeon 6152</td>
<td>44</td>
<td>377 GB</td>
<td>—</td>
<td><code>csaxs</code></td>
</tr>
<tr>
<td><code>ra-gpu-003</code></td>
<td>AMD EPYC 7452</td>
<td>64</td>
<td>1007 GB</td>
<td>4x NVIDIA A100 (40 GB)</td>
<td><code>gpu-csaxs</code></td>
</tr>
<tr>
<td><code>ra-gpu-007</code></td>
<td>Intel Xeon 6530</td>
<td>64</td>
<td>1007 GB</td>
<td>4x NVIDIA L40S (46 GB)</td>
<td><code>gpu-csaxs</code></td>
</tr>
</tbody>
</table>
<p><strong>The home directory is the p group.</strong> To go to the raw directory we need to navigate there:</p>
<div class="highlight"><pre><span></span><code><span class="nb">cd</span><span class="w"> </span>/sls/x12sa/data/<span class="o">[</span>p22598<span class="o">]</span>/raw
</code></pre></div>
<h2 id="python-tools">Python tools<a class="headerlink" href="#python-tools" title="Permanent link">&para;</a></h2>
<h3 id="python-package-installation">Python package installation<a class="headerlink" href="#python-package-installation" title="Permanent link">&para;</a></h3>
<p>Anaconda is no longer supported. Packages should now be installed directly using <code>pip</code>.</p>
<p>For example, <code>pyFAI</code> can be installed as follows:</p>
<div class="highlight"><pre><span></span><code>module<span class="w"> </span>load<span class="w"> </span>Python/3.11.11
pip<span class="w"> </span>install<span class="w"> </span><span class="s2">&quot;pyFAI[gui]&quot;</span>
</code></pre></div>
<p>To launch the <code>pyFAI</code> applications:</p>
<div class="highlight"><pre><span></span><code><span class="c1"># Detector calibration</span>
python<span class="w"> </span>-m<span class="w"> </span>pyFAI.app.calib2
<span class="c1"># Batch integration</span>
python<span class="w"> </span>-m<span class="w"> </span>pyFAI.app.integrate
</code></pre></div>
<h3 id="recommended-using-a-python-virtual-environment">Recommended: using a Python virtual environment<a class="headerlink" href="#recommended-using-a-python-virtual-environment" title="Permanent link">&para;</a></h3>
<p>For long-term maintainability and reproducibility, it is recommended to use a dedicated Python virtual environment.</p>
<h4 id="create-a-virtual-environment">Create a virtual environment<a class="headerlink" href="#create-a-virtual-environment" title="Permanent link">&para;</a></h4>
<div class="highlight"><pre><span></span><code><span class="nb">cd</span><span class="w"> </span>/sls/x12sa/data/<span class="o">[</span>p-group<span class="o">]</span>/raw
module<span class="w"> </span>load<span class="w"> </span>Python/3.11.11
mkdir<span class="w"> </span>python-env
<span class="nb">cd</span><span class="w"> </span>python-env
<span class="c1"># Create a virtual environment named &quot;.venv&quot;</span>
python3<span class="w"> </span>-m<span class="w"> </span>venv<span class="w"> </span>.venv
<span class="c1"># Activate the environment</span>
<span class="nb">source</span><span class="w"> </span>.venv/bin/activate
<span class="c1"># Install required packages</span>
pip<span class="w"> </span>install<span class="w"> </span><span class="s2">&quot;pyFAI[gui]&quot;</span>
</code></pre></div>
<h4 id="use-an-existing-virtual-environment">Use an existing virtual environment<a class="headerlink" href="#use-an-existing-virtual-environment" title="Permanent link">&para;</a></h4>
<div class="highlight"><pre><span></span><code><span class="nb">cd</span><span class="w"> </span>/sls/x12sa/data/<span class="o">[</span>p-group<span class="o">]</span>/raw/python-env
<span class="nb">source</span><span class="w"> </span>.venv/bin/activate
</code></pre></div>
<h4 id="troubleshooting">Troubleshooting<a class="headerlink" href="#troubleshooting" title="Permanent link">&para;</a></h4>
<p>If you encounter the following error when launching GUI applications (e.g. <code>pyFAI-calib2</code>):</p>
<div class="highlight"><pre><span></span><code>X11 connection rejected
</code></pre></div>
<p>reconnect to the analysis node with X11 forwarding enabled:</p>
<div class="highlight"><pre><span></span><code>ssh<span class="w"> </span>-X<span class="w"> </span><span class="o">[</span>ra-c-110<span class="o">]</span>
</code></pre></div>
<p>and then reactivate the virtual environment before launching the application.</p>
<h3 id="use-jupyter-notebook-lab">Use Jupyter Notebook / Lab<a class="headerlink" href="#use-jupyter-notebook-lab" title="Permanent link">&para;</a></h3>
<p>Create a virtual environment following the instructions above, then:</p>
<div class="highlight"><pre><span></span><code>pip<span class="w"> </span>install<span class="w"> </span>jupyter
</code></pre></div>
<p>To run Jupyter Lab:</p>
<div class="highlight"><pre><span></span><code>jupyter<span class="w"> </span>lab<span class="w"> </span>--port<span class="w"> </span><span class="m">6006</span><span class="w"> </span>--ip<span class="w"> </span><span class="k">$(</span>hostname<span class="k">)</span><span class="w"> </span>--no-browser
</code></pre></div>
<h2 id="csaxs-matlab-scripts">cSAXS matlab scripts<a class="headerlink" href="#csaxs-matlab-scripts" title="Permanent link">&para;</a></h2>
<p>To use the cSAXS matlab scripts we can go to the <code>cxs_software</code> package in the raw folder. </p>
<p>In base we can do:
<div class="highlight"><pre><span></span><code><span class="nb">source</span><span class="w"> </span>setup-environment.sh<span class="w"> </span>
</code></pre></div>
And then we can use Matlab interactively as usual.
<div class="highlight"><pre><span></span><code>matlab<span class="w"> </span><span class="p">&amp;</span>
</code></pre></div></p>
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