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labordynamicsinstitute · Oct 19, 2024 · d17090f · d17090f
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diff --git a/_sources/docs/biohpc/slurm-quick-start.md b/_sources/docs/biohpc/slurm-quick-start.md
@@ -15,10 +15,15 @@ From a command line, run the following lines, logout, then back in, and hencefor
 
 ```bash
 echo 'export SLURM_CLUSTERS="cbsueccosl01"' >> $HOME/.bash_profile
+```
+
+In the following, replace `netid` with your actual NetID. 
+
+
+```bash
 echo [email protected] >> $HOME/.forward
 ``` 
 
-(replace your `netid` in the second command).
 
 ### Enabling software via `module`
 
@@ -59,6 +64,28 @@ If you need a specific node, use
 srun -w cbsueccoXX --pty bash -l
 ```
 
+## Interactive GUI jobs
+
+You should be able to get interactive GUI jobs (Stata, MATLAB) to work as follows:
+
+```bash
+salloc -N 1 
+ssh -X $SLURM_NODELIST /usr/local/stata18/xstata
+```
+
+or 
+
+```bash
+salloc -N 1 
+ssh -X $SLURM_NODELIST /local/opt/MATLAB/R2023a/bin/matlab
+```
+
+:::{warning}
+
+It is technically feasible to login to each node without using SLURM. However, this confuses the job scheduler. Do not abuse this, exclusion from use of the cluster may be the consequence.
+
+:::
+
 ## To see running jobs
 
 ```
@@ -77,4 +104,4 @@ where the ID can be gleaned from the `squeue` command.
 
 ## Additional information
 
-- [https://biohpc.cornell.edu/lab/SLURM-on-demand.htm](https://biohpc.cornell.edu/lab/SLURM-on-demand.htm)
+- [https://biohpc.cornell.edu/lab/SLURM-on-demand.htm](https://biohpc.cornell.edu/lab/SLURM-on-demand.htm)
diff --git a/docs/biohpc/slurm-quick-start.html b/docs/biohpc/slurm-quick-start.html
@@ -439,6 +439,7 @@ <h2> Contents </h2>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submitting-jobs">Submitting jobs</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#interactive-shell">Interactive shell</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#interactive-gui-jobs">Interactive GUI jobs</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#to-see-running-jobs">To see running jobs</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#to-cancel-a-running-job">To cancel a running job</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#additional-information">Additional information</a></li>
@@ -465,10 +466,12 @@ <h2>Command line<a class="headerlink" href="#command-line" title="Link to this h
 <h3>Setting up SLURM-specific settings<a class="headerlink" href="#setting-up-slurm-specific-settings" title="Link to this heading">#</a></h3>
 <p>From a command line, run the following lines, logout, then back in, and henceforth you can skip the <code class="docutils literal notranslate"><span class="pre">--cluster</span> <span class="pre">cbsueccosl01</span></code> option:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;export SLURM_CLUSTERS=&quot;cbsueccosl01&quot;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span><span class="nv">$HOME</span>/.bash_profile
-<span class="nb">echo</span><span class="w"> </span>[email protected]<span class="w"> </span>&gt;&gt;<span class="w"> </span><span class="nv">$HOME</span>/.forward
 </pre></div>
 </div>
-<p>(replace your <code class="docutils literal notranslate"><span class="pre">netid</span></code> in the second command).</p>
+<p>In the following, replace <code class="docutils literal notranslate"><span class="pre">netid</span></code> with your actual NetID.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span>[email protected]<span class="w"> </span>&gt;&gt;<span class="w"> </span><span class="nv">$HOME</span>/.forward
+</pre></div>
+</div>
 </section>
 <section id="enabling-software-via-module">
 <h3>Enabling software via <code class="docutils literal notranslate"><span class="pre">module</span></code><a class="headerlink" href="#enabling-software-via-module" title="Link to this heading">#</a></h3>
@@ -502,6 +505,23 @@ <h2>Interactive shell<a class="headerlink" href="#interactive-shell" title="Link
 </pre></div>
 </div>
 </section>
+<section id="interactive-gui-jobs">
+<h2>Interactive GUI jobs<a class="headerlink" href="#interactive-gui-jobs" title="Link to this heading">#</a></h2>
+<p>You should be able to get interactive GUI jobs (Stata, MATLAB) to work as follows:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>salloc<span class="w"> </span>-N<span class="w"> </span><span class="m">1</span><span class="w"> </span>
+ssh<span class="w"> </span>-X<span class="w"> </span><span class="nv">$SLURM_NODELIST</span><span class="w"> </span>/usr/local/stata18/xstata
+</pre></div>
+</div>
+<p>or</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>salloc<span class="w"> </span>-N<span class="w"> </span><span class="m">1</span><span class="w"> </span>
+ssh<span class="w"> </span>-X<span class="w"> </span><span class="nv">$SLURM_NODELIST</span><span class="w"> </span>/local/opt/MATLAB/R2023a/bin/matlab
+</pre></div>
+</div>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>It is technically feasible to login to each node without using SLURM. However, this confuses the job scheduler. Do not abuse this, exclusion from use of the cluster may be the consequence.</p>
+</div>
+</section>
 <section id="to-see-running-jobs">
 <h2>To see running jobs<a class="headerlink" href="#to-see-running-jobs" title="Link to this heading">#</a></h2>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">squeue</span>
@@ -596,6 +616,7 @@ <h2>Additional information<a class="headerlink" href="#additional-information" t
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submitting-jobs">Submitting jobs</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#interactive-shell">Interactive shell</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#interactive-gui-jobs">Interactive GUI jobs</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#to-see-running-jobs">To see running jobs</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#to-cancel-a-running-job">To cancel a running job</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#additional-information">Additional information</a></li>

diff --git a/docs/biohpc/slurm.html b/docs/biohpc/slurm.html
diff --git a/docs/linux.html b/docs/linux.html
@@ -504,7 +504,7 @@ <h2>Available resources<a class="headerlink" href="#available-resources" title="
 <p><strong>Details:</strong></p>
 <div class="cell tag_remove-input tag_full-width docutils container">
 <div class="cell_output docutils container">
-<div class="output text_html"><table id="itables_7d84b408_b421_44be_8183_acb30dd2ddb8" class="display compact" data-quarto-disable-processing="true" style="table-layout:auto;width:auto;margin:auto;caption-side:bottom">
+<div class="output text_html"><table id="itables_82884f14_6e01_4738_82fd_e6a12b150477" class="display compact" data-quarto-disable-processing="true" style="table-layout:auto;width:auto;margin:auto;caption-side:bottom">
 <thead>
     <tr style="text-align: right;">
 
@@ -525,7 +525,7 @@ <h2>Available resources<a class="headerlink" href="#available-resources" title="
 <script type="module">
     const { DataTable, jQuery: $ } = await import(window._datatables_src_for_itables_2_0_0);
 
-    document.querySelectorAll("#itables_7d84b408_b421_44be_8183_acb30dd2ddb8:not(.dataTable)").forEach(table => {
+    document.querySelectorAll("#itables_82884f14_6e01_4738_82fd_e6a12b150477:not(.dataTable)").forEach(table => {
         // Define the table data
         const data = [["cbsuecco01", "reservation", 1939.0, 32, 256, 0.2, "Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz", 16, 2, 2017.0], ["cbsuecco02", "reservation", 1284.0, 32, 1024, 4.3, "Intel(R) Xeon(R) CPU E7- 8837 @ 2.67GHz", 8, 4, 2011.0], ["cbsuecco03", "flex", 1091.0, 32, 256, 1.4, "AMD Opteron(tm) Processor 6380", 16, 2, 2011.0], ["cbsuecco04", "flex", 1091.0, 32, 256, 1.4, "AMD Opteron(tm) Processor 6380", 16, 2, 2011.0], ["cbsuecco05", "flex", 1091.0, 32, 256, 1.4, "AMD Opteron(tm) Processor 6380", 16, 2, 2011.0], ["cbsuecco06", "flex", NaN, 64, 256, 2.6, "NaN", 32, 2, NaN], ["cbsuecco07", "flex", 1952.0, 28, 128, 0.2, "Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz", 14, 2, 2016.0], ["cbsuecco08", "flex", 1952.0, 28, 128, 0.2, "Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz", 14, 2, 2016.0], ["cbsuecco09", "flex", 3418.0, 56, 256, 3.5, "Intel(R) Xeon(R) Gold 5420+ @ 2.0-4.1GHz", 28, 2, 2024.0], ["cbsuecco10", "flex", 3418.0, 56, 256, 3.5, "Intel(R) Xeon(R) Gold 5420+ @ 2.0-4.1GHz", 28, 2, 2024.0], ["cbsuecco11", "flex", 3418.0, 56, 256, 3.5, "Intel(R) Xeon(R) Gold 5420+ @ 2.0-4.1GHz", 28, 2, 2024.0], ["cbsuecco12", "flex", 3418.0, 56, 256, 3.5, "Intel(R) Xeon(R) Gold 5420+ @ 2.0-4.1GHz", 28, 2, 2024.0], ["cbsueccosl01", "slurm", 1091.0, 16, 128, 6.9, "AMD Opteron(tm) Processor 6380", 16, 1, 2011.0], ["cbsueccosl04", "slurm", 1091.0, 32, 256, 5.0, "AMD Opteron(tm) Processor 6380", 16, 2, 2011.0]];
 

diff --git a/searchindex.js b/searchindex.js