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laszewsk committed Nov 17, 2023
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12 changes: 11 additions & 1 deletion uva/docs/_print/index.html
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Expand Up @@ -19331,7 +19331,9 @@ <h1 id="pg-de0dac4e9a919562224c35394e294222">4.2 - Rivanna</h1>

<h2 id="communication">Communication</h2>
<p>We have a team discord at: uva-bii-community</p>
<p><a href="https://discord.gg/uFKJ5TUv">https://discord.gg/uFKJ5TUv</a></p>
<p><a href="https://discord.gg/7K2PQqxYz7">https://discord.gg/7K2PQqxYz7</a></p>
<p>to be added, send <a href="mailto:[email protected]">[email protected]</a> an email with subject:
Please add me to discord for bii_dsc_community</p>
<p>please subscribe if you work on rivanna and are part of the
bii_dsc_community.</p>
<h2 id="rivanna-at-uva">Rivanna at UVA</h2>
Expand Down Expand Up @@ -19985,6 +19987,10 @@ <h2 id="linux-commands-for-hpc">Linux commands for HPC</h2>
<td>check available account and balance</td>
</tr>
<tr>
<td><code>allocations -a bii_dsc_community</code></td>
<td>check allocation availability for users under <code>bii_dsc_community</code></td>
</tr>
<tr>
<td><code>hdquota</code></td>
<td>check storage you has used</td>
</tr>
Expand Down Expand Up @@ -20235,6 +20241,10 @@ <h3 id="singularity-cache">Singularity cache</h3>
<div class="highlight"><pre tabindex="0" style="background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>rivanna&gt;
</span></span><span style="display:flex;"><span> mkdir -p /scratch/<span style="color:#000">$USER</span>/.singularity/cache
</span></span><span style="display:flex;"><span> <span style="color:#204a87">export</span> <span style="color:#000">SINGULARITY_CACHEDIR</span><span style="color:#ce5c00;font-weight:bold">=</span>/scratch/<span style="color:#000">$USER</span>/.singularity/cache
</span></span></code></pre></div><p>Please remember that scratch is not permanent. In case you like a bit more permanent location you can alternatively use</p>
<div class="highlight"><pre tabindex="0" style="background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>rivanna&gt;
</span></span><span style="display:flex;"><span> mkdir -p /project/bii_dsc_community/<span style="color:#000">$USER</span>/.singularity/cache
</span></span><span style="display:flex;"><span> <span style="color:#204a87">export</span> <span style="color:#000">SINGULARITY_CACHEDIR</span><span style="color:#ce5c00;font-weight:bold">=</span>/project/bii_dsc_community/<span style="color:#000">$USER</span>/.singularity/cache
</span></span></code></pre></div><h3 id="builddef">build.def</h3>
<p>To build an image you will need a build definition file</p>
<p>We show next an exxample of a simple <code>buid.def</code> file that uses
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12 changes: 11 additions & 1 deletion uva/docs/index.xml
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Expand Up @@ -1097,7 +1097,9 @@ A100-40GB, A100-80GB.&lt;/p&gt;

&lt;h2 id=&#34;communication&#34;&gt;Communication&lt;/h2&gt;
&lt;p&gt;We have a team discord at: uva-bii-community&lt;/p&gt;
&lt;p&gt;&lt;a href=&#34;https://discord.gg/uFKJ5TUv&#34;&gt;https://discord.gg/uFKJ5TUv&lt;/a&gt;&lt;/p&gt;
&lt;p&gt;&lt;a href=&#34;https://discord.gg/7K2PQqxYz7&#34;&gt;https://discord.gg/7K2PQqxYz7&lt;/a&gt;&lt;/p&gt;
&lt;p&gt;to be added, send &lt;a href=&#34;mailto:[email protected]&#34;&gt;[email protected]&lt;/a&gt; an email with subject:
Please add me to discord for bii_dsc_community&lt;/p&gt;
&lt;p&gt;please subscribe if you work on rivanna and are part of the
bii_dsc_community.&lt;/p&gt;
&lt;h2 id=&#34;rivanna-at-uva&#34;&gt;Rivanna at UVA&lt;/h2&gt;
Expand Down Expand Up @@ -1751,6 +1753,10 @@ partitons use &lt;code&gt;qlist&lt;/code&gt; to check partitions&lt;/p&gt;
&lt;td&gt;check available account and balance&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;allocations -a bii_dsc_community&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;check allocation availability for users under &lt;code&gt;bii_dsc_community&lt;/code&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;hdquota&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;check storage you has used&lt;/td&gt;
&lt;/tr&gt;
Expand Down Expand Up @@ -1993,6 +1999,10 @@ set it as follows&lt;/p&gt;
&lt;div class=&#34;highlight&#34;&gt;&lt;pre tabindex=&#34;0&#34; style=&#34;background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;&#34;&gt;&lt;code class=&#34;language-bash&#34; data-lang=&#34;bash&#34;&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt;rivanna&amp;gt;
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; mkdir -p /scratch/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; &lt;span style=&#34;color:#204a87&#34;&gt;export&lt;/span&gt; &lt;span style=&#34;color:#000&#34;&gt;SINGULARITY_CACHEDIR&lt;/span&gt;&lt;span style=&#34;color:#ce5c00;font-weight:bold&#34;&gt;=&lt;/span&gt;/scratch/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/div&gt;&lt;p&gt;Please remember that scratch is not permanent. In case you like a bit more permanent location you can alternatively use&lt;/p&gt;
&lt;div class=&#34;highlight&#34;&gt;&lt;pre tabindex=&#34;0&#34; style=&#34;background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;&#34;&gt;&lt;code class=&#34;language-bash&#34; data-lang=&#34;bash&#34;&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt;rivanna&amp;gt;
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; mkdir -p /project/bii_dsc_community/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; &lt;span style=&#34;color:#204a87&#34;&gt;export&lt;/span&gt; &lt;span style=&#34;color:#000&#34;&gt;SINGULARITY_CACHEDIR&lt;/span&gt;&lt;span style=&#34;color:#ce5c00;font-weight:bold&#34;&gt;=&lt;/span&gt;/project/bii_dsc_community/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/div&gt;&lt;h3 id=&#34;builddef&#34;&gt;build.def&lt;/h3&gt;
&lt;p&gt;To build an image you will need a build definition file&lt;/p&gt;
&lt;p&gt;We show next an exxample of a simple &lt;code&gt;buid.def&lt;/code&gt; file that uses
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12 changes: 11 additions & 1 deletion uva/docs/tutorial/_print/index.html
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Expand Up @@ -468,7 +468,9 @@ <h1 id="pg-de0dac4e9a919562224c35394e294222">2 - Rivanna</h1>

<h2 id="communication">Communication</h2>
<p>We have a team discord at: uva-bii-community</p>
<p><a href="https://discord.gg/uFKJ5TUv">https://discord.gg/uFKJ5TUv</a></p>
<p><a href="https://discord.gg/7K2PQqxYz7">https://discord.gg/7K2PQqxYz7</a></p>
<p>to be added, send <a href="mailto:[email protected]">[email protected]</a> an email with subject:
Please add me to discord for bii_dsc_community</p>
<p>please subscribe if you work on rivanna and are part of the
bii_dsc_community.</p>
<h2 id="rivanna-at-uva">Rivanna at UVA</h2>
Expand Down Expand Up @@ -1122,6 +1124,10 @@ <h2 id="linux-commands-for-hpc">Linux commands for HPC</h2>
<td>check available account and balance</td>
</tr>
<tr>
<td><code>allocations -a bii_dsc_community</code></td>
<td>check allocation availability for users under <code>bii_dsc_community</code></td>
</tr>
<tr>
<td><code>hdquota</code></td>
<td>check storage you has used</td>
</tr>
Expand Down Expand Up @@ -1372,6 +1378,10 @@ <h3 id="singularity-cache">Singularity cache</h3>
<div class="highlight"><pre tabindex="0" style="background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>rivanna&gt;
</span></span><span style="display:flex;"><span> mkdir -p /scratch/<span style="color:#000">$USER</span>/.singularity/cache
</span></span><span style="display:flex;"><span> <span style="color:#204a87">export</span> <span style="color:#000">SINGULARITY_CACHEDIR</span><span style="color:#ce5c00;font-weight:bold">=</span>/scratch/<span style="color:#000">$USER</span>/.singularity/cache
</span></span></code></pre></div><p>Please remember that scratch is not permanent. In case you like a bit more permanent location you can alternatively use</p>
<div class="highlight"><pre tabindex="0" style="background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>rivanna&gt;
</span></span><span style="display:flex;"><span> mkdir -p /project/bii_dsc_community/<span style="color:#000">$USER</span>/.singularity/cache
</span></span><span style="display:flex;"><span> <span style="color:#204a87">export</span> <span style="color:#000">SINGULARITY_CACHEDIR</span><span style="color:#ce5c00;font-weight:bold">=</span>/project/bii_dsc_community/<span style="color:#000">$USER</span>/.singularity/cache
</span></span></code></pre></div><h3 id="builddef">build.def</h3>
<p>To build an image you will need a build definition file</p>
<p>We show next an exxample of a simple <code>buid.def</code> file that uses
Expand Down
12 changes: 11 additions & 1 deletion uva/docs/tutorial/index.xml
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Expand Up @@ -259,7 +259,9 @@ A100-40GB, A100-80GB.&lt;/p&gt;

&lt;h2 id=&#34;communication&#34;&gt;Communication&lt;/h2&gt;
&lt;p&gt;We have a team discord at: uva-bii-community&lt;/p&gt;
&lt;p&gt;&lt;a href=&#34;https://discord.gg/uFKJ5TUv&#34;&gt;https://discord.gg/uFKJ5TUv&lt;/a&gt;&lt;/p&gt;
&lt;p&gt;&lt;a href=&#34;https://discord.gg/7K2PQqxYz7&#34;&gt;https://discord.gg/7K2PQqxYz7&lt;/a&gt;&lt;/p&gt;
&lt;p&gt;to be added, send &lt;a href=&#34;mailto:[email protected]&#34;&gt;[email protected]&lt;/a&gt; an email with subject:
Please add me to discord for bii_dsc_community&lt;/p&gt;
&lt;p&gt;please subscribe if you work on rivanna and are part of the
bii_dsc_community.&lt;/p&gt;
&lt;h2 id=&#34;rivanna-at-uva&#34;&gt;Rivanna at UVA&lt;/h2&gt;
Expand Down Expand Up @@ -913,6 +915,10 @@ partitons use &lt;code&gt;qlist&lt;/code&gt; to check partitions&lt;/p&gt;
&lt;td&gt;check available account and balance&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;allocations -a bii_dsc_community&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;check allocation availability for users under &lt;code&gt;bii_dsc_community&lt;/code&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;hdquota&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;check storage you has used&lt;/td&gt;
&lt;/tr&gt;
Expand Down Expand Up @@ -1155,6 +1161,10 @@ set it as follows&lt;/p&gt;
&lt;div class=&#34;highlight&#34;&gt;&lt;pre tabindex=&#34;0&#34; style=&#34;background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;&#34;&gt;&lt;code class=&#34;language-bash&#34; data-lang=&#34;bash&#34;&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt;rivanna&amp;gt;
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; mkdir -p /scratch/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; &lt;span style=&#34;color:#204a87&#34;&gt;export&lt;/span&gt; &lt;span style=&#34;color:#000&#34;&gt;SINGULARITY_CACHEDIR&lt;/span&gt;&lt;span style=&#34;color:#ce5c00;font-weight:bold&#34;&gt;=&lt;/span&gt;/scratch/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/div&gt;&lt;p&gt;Please remember that scratch is not permanent. In case you like a bit more permanent location you can alternatively use&lt;/p&gt;
&lt;div class=&#34;highlight&#34;&gt;&lt;pre tabindex=&#34;0&#34; style=&#34;background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;&#34;&gt;&lt;code class=&#34;language-bash&#34; data-lang=&#34;bash&#34;&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt;rivanna&amp;gt;
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; mkdir -p /project/bii_dsc_community/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;span style=&#34;display:flex;&#34;&gt;&lt;span&gt; &lt;span style=&#34;color:#204a87&#34;&gt;export&lt;/span&gt; &lt;span style=&#34;color:#000&#34;&gt;SINGULARITY_CACHEDIR&lt;/span&gt;&lt;span style=&#34;color:#ce5c00;font-weight:bold&#34;&gt;=&lt;/span&gt;/project/bii_dsc_community/&lt;span style=&#34;color:#000&#34;&gt;$USER&lt;/span&gt;/.singularity/cache
&lt;/span&gt;&lt;/span&gt;&lt;/code&gt;&lt;/pre&gt;&lt;/div&gt;&lt;h3 id=&#34;builddef&#34;&gt;build.def&lt;/h3&gt;
&lt;p&gt;To build an image you will need a build definition file&lt;/p&gt;
&lt;p&gt;We show next an exxample of a simple &lt;code&gt;buid.def&lt;/code&gt; file that uses
Expand Down
16 changes: 11 additions & 5 deletions uva/docs/tutorial/rivanna/index.html
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Expand Up @@ -27,12 +27,12 @@
<meta property="og:type" content="article" />
<meta property="og:url" content="https://infomall.org/uva/docs/tutorial/rivanna/" /><meta property="article:section" content="docs" />

<meta property="article:modified_time" content="2023-07-28T11:13:06-04:00" /><meta property="og:site_name" content="Infomall.org" />
<meta property="article:modified_time" content="2023-10-07T16:42:13-04:00" /><meta property="og:site_name" content="Infomall.org" />
<meta itemprop="name" content="Rivanna">
<meta itemprop="description" content="Rivanna
">
<meta itemprop="dateModified" content="2023-07-28T11:13:06-04:00" />
<meta itemprop="wordCount" content="2930">
<meta itemprop="dateModified" content="2023-10-07T16:42:13-04:00" />
<meta itemprop="wordCount" content="2956">
<meta itemprop="keywords" content="" /><meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Rivanna"/>
<meta name="twitter:description" content="Rivanna
Expand Down Expand Up @@ -344,7 +344,9 @@ <h1>Rivanna</h1>

<h2 id="communication">Communication</h2>
<p>We have a team discord at: uva-bii-community</p>
<p><a href="https://discord.gg/uFKJ5TUv">https://discord.gg/uFKJ5TUv</a></p>
<p><a href="https://discord.gg/7K2PQqxYz7">https://discord.gg/7K2PQqxYz7</a></p>
<p>to be added, send <a href="mailto:[email protected]">[email protected]</a> an email with subject:
Please add me to discord for bii_dsc_community</p>
<p>please subscribe if you work on rivanna and are part of the
bii_dsc_community.</p>
<h2 id="rivanna-at-uva">Rivanna at UVA</h2>
Expand Down Expand Up @@ -998,6 +1000,10 @@ <h2 id="linux-commands-for-hpc">Linux commands for HPC</h2>
<td>check available account and balance</td>
</tr>
<tr>
<td><code>allocations -a bii_dsc_community</code></td>
<td>check allocation availability for users under <code>bii_dsc_community</code></td>
</tr>
<tr>
<td><code>hdquota</code></td>
<td>check storage you has used</td>
</tr>
Expand Down Expand Up @@ -1092,7 +1098,7 @@ <h2 id="help-support">Help Support</h2>


<div class="text-muted mt-5 pt-3 border-top">
Last modified July 28, 2023: <a href="https://github.com/DSC-SPIDAL/infomall-org-uva/commit/bfc73a27c6fe4d2e633278da85f17c92188d1ad7">Update rivanna.md (bfc73a2)</a>
Last modified October 7, 2023: <a href="https://github.com/DSC-SPIDAL/infomall-org-uva/commit/99432ec895665a2f5c637ce47f1136aa460b8588">Update rivanna.md (99432ec)</a>
</div>

</div>
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12 changes: 8 additions & 4 deletions uva/docs/tutorial/singularity/index.html
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Expand Up @@ -25,11 +25,11 @@
<meta property="og:type" content="article" />
<meta property="og:url" content="https://infomall.org/uva/docs/tutorial/singularity/" /><meta property="article:section" content="docs" />

<meta property="article:modified_time" content="2023-07-24T18:53:13-04:00" /><meta property="og:site_name" content="Infomall.org" />
<meta property="article:modified_time" content="2023-08-17T11:11:31-04:00" /><meta property="og:site_name" content="Infomall.org" />
<meta itemprop="name" content="Rivanna and Singularity">
<meta itemprop="description" content="Singularity.">
<meta itemprop="dateModified" content="2023-07-24T18:53:13-04:00" />
<meta itemprop="wordCount" content="639">
<meta itemprop="dateModified" content="2023-08-17T11:11:31-04:00" />
<meta itemprop="wordCount" content="665">
<meta itemprop="keywords" content="" /><meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Rivanna and Singularity"/>
<meta name="twitter:description" content="Singularity."/>
Expand Down Expand Up @@ -340,6 +340,10 @@ <h3 id="singularity-cache">Singularity cache</h3>
<div class="highlight"><pre tabindex="0" style="background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>rivanna&gt;
</span></span><span style="display:flex;"><span> mkdir -p /scratch/<span style="color:#000">$USER</span>/.singularity/cache
</span></span><span style="display:flex;"><span> <span style="color:#204a87">export</span> <span style="color:#000">SINGULARITY_CACHEDIR</span><span style="color:#ce5c00;font-weight:bold">=</span>/scratch/<span style="color:#000">$USER</span>/.singularity/cache
</span></span></code></pre></div><p>Please remember that scratch is not permanent. In case you like a bit more permanent location you can alternatively use</p>
<div class="highlight"><pre tabindex="0" style="background-color:#f8f8f8;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>rivanna&gt;
</span></span><span style="display:flex;"><span> mkdir -p /project/bii_dsc_community/<span style="color:#000">$USER</span>/.singularity/cache
</span></span><span style="display:flex;"><span> <span style="color:#204a87">export</span> <span style="color:#000">SINGULARITY_CACHEDIR</span><span style="color:#ce5c00;font-weight:bold">=</span>/project/bii_dsc_community/<span style="color:#000">$USER</span>/.singularity/cache
</span></span></code></pre></div><h3 id="builddef">build.def</h3>
<p>To build an image you will need a build definition file</p>
<p>We show next an exxample of a simple <code>buid.def</code> file that uses
Expand Down Expand Up @@ -440,7 +444,7 @@ <h3 id="running-on-special-fox-node-a100-80gb">RUnning on special fox node a100-


<div class="text-muted mt-5 pt-3 border-top">
Last modified July 24, 2023: <a href="https://github.com/DSC-SPIDAL/infomall-org-uva/commit/934c9bd8df6f9dee505fb9d8648cea5af8ce2baf">Update singularity.md (934c9bd)</a>
Last modified August 17, 2023: <a href="https://github.com/DSC-SPIDAL/infomall-org-uva/commit/c6eccf97d359b9311b4fdb932bee9276b54391fc">Update singularity.md (c6eccf9)</a>
</div>

</div>
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Expand Up @@ -69,7 +69,7 @@
<lastmod>2023-03-31T07:48:53-04:00</lastmod>
</url><url>
<loc>https://infomall.org/uva/docs/tutorial/rivanna/</loc>
<lastmod>2023-07-28T11:13:06-04:00</lastmod>
<lastmod>2023-10-07T16:42:13-04:00</lastmod>
</url><url>
<loc>https://infomall.org/uva/docs/tutorial/rivanna-superpod/</loc>
<lastmod>2023-07-13T08:18:58-04:00</lastmod>
Expand All @@ -84,7 +84,7 @@
<lastmod>2023-03-22T16:55:24-04:00</lastmod>
</url><url>
<loc>https://infomall.org/uva/docs/tutorial/singularity/</loc>
<lastmod>2023-07-24T18:53:13-04:00</lastmod>
<lastmod>2023-08-17T11:11:31-04:00</lastmod>
</url><url>
<loc>https://infomall.org/uva/docs/staff/</loc>
<lastmod>2023-03-22T16:55:24-04:00</lastmod>
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