Skip to content

Commit 7721078

Browse files
committed
Deploy preview for PR 32 🛫
1 parent dda9f7b commit 7721078

File tree

3 files changed

+33
-35
lines changed

3 files changed

+33
-35
lines changed

pr-preview/pr-32/admin/ondemand/index.html

Lines changed: 26 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -2157,36 +2157,34 @@ <h2 id="admin-troublshooting">Admin Troublshooting<a class="headerlink" href="#a
21572157
<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a> oodapp-&gt;&gt;user: render
21582158
</code></pre></div>
21592159
<ol>
2160-
<li>
2161-
<p>Apache
2162-
To start, all users who navigate to the ondemand website first encounter the apache server. Any errors encountered at this step will be in the log(s) at <code>/var/log/apache2/error.log</code></p>
2163-
</li>
2164-
<li>
2165-
<p>CAS
2166-
Apache then redirects the users to CAS for authentication. You can <code>grep -r $user /var/cache/apache2/mod_auth_cas/</code> to check if users have been authed to CAS and a cookie has been set.</p>
2167-
</li>
2168-
<li>
2169-
<p>Apache part deux
2170-
CAS brings us back to apache and here apache runs all sorts of OOD Lua hooks. Any errors encountered at this step will be in the l
2160+
<li>Apache</li>
2161+
</ol>
2162+
<p>To start, all users who navigate to the ondemand website first encounter the apache server. Any errors encountered at this step will be in the log(s) at <code>/var/log/apache2/error.log</code></p>
2163+
<ol>
2164+
<li>CAS</li>
2165+
</ol>
2166+
<p>Apache then redirects the users to CAS for authentication. You can <code>grep -r $user /var/cache/apache2/mod_auth_cas/</code> to check if users have been authed to CAS and a cookie has been set.</p>
2167+
<ol>
2168+
<li>Apache part deux</li>
2169+
</ol>
2170+
<p>CAS brings us back to apache and here apache runs all sorts of OOD Lua hooks. Any errors encountered at this step will be in the l
21712171
og(s) at <code>/var/log/apache2/$fqdn_error.log</code></p>
2172-
</li>
2173-
<li>
2174-
<p>The PUN (Per User Nginx) session
2175-
Apache then starts an NginX server as the user and most things like the main dashboard, submitting jobs, running apps, etc happen here in the PUN. Any errors encountered at this step will be in the logs at <code>/var/log/ondemand-nginx/$user/error.log</code>. You can also see what might be happening here by running commands like <code>ps aux | grep $USER</code> to see the users PUN, or <code>ps aux | grep -i nginx</code> to see all the PUNs. From the ondemand web UI theres an option to "Restart Web Server" which essentially kills and restarts the users PUN.</p>
2176-
</li>
2177-
<li>
2178-
<p>/pun/sys/dashboard
2179-
The dashboard is mostly covered in section 4, but just wanted to denote that apache then redirects us here after the PUN has been started where users can do everything else. At this step OOD will warn you about things like "Home Directory Not Found" and such. If you get this far I'd recommend you troubleshoot issues with users' home dir, NASii, and free space: <code>df | grep $HOME</code>, <code>du -sh $HOME</code>, <code>journalctl -u autofs</code>, and umount stuff. Check that <code>$HOME/ondemand</code> exists perhaps.</p>
2180-
</li>
2181-
<li>
2182-
<p>OOD Apps
2183-
When users start an app like JuyterLab or a VNC desktop the job is submitted by the users' PUN and here OOD copies and renders (with ERB) the global app template from <code>/var/www/ood/apps/sys/&lt;app_name&gt;/template/*</code> to <code>$HOME/ondemand/data/sys/dashboard/batch_connect/sys/&lt;app_name&gt;/(output)/&lt;session_id&gt;</code>. Any errors encountered at this step will be in <code>$HOME/ondemand/data/sys/dashboard/batch_connect/sys/&lt;app_name&gt;/(output)/&lt;session_id&gt;/*.log</code>.</p>
2184-
</li>
2185-
<li>
2186-
<p>Misc
2187-
Maybe the ondemand server is just in some invalid state and needs to be reset. I'd recommend you check the puppet conf at <code>/etc/puppetlabs/puppet/puppet.conf</code>, run <code>puppet agent -t</code> , and maybe restart the machine. Running puppet will force restart the apache server and regenerate OOD from the ood config yamls. Then you can restart the server by either ssh-ing to the server and running <code>reboot</code>, or by ssh-ing to proxmox and running <code>qm reset &lt;vmid&gt;</code> as root. TIP: you can find the vmid by finding the server in <code>qm list</code>. </p>
2188-
</li>
2172+
<ol>
2173+
<li>The PUN (Per User Nginx) session</li>
2174+
</ol>
2175+
<p>Apache then starts an NginX server as the user and most things like the main dashboard, submitting jobs, running apps, etc happen here in the PUN. Any errors encountered at this step will be in the logs at <code>/var/log/ondemand-nginx/$user/error.log</code>. You can also see what might be happening here by running commands like <code>ps aux | grep $USER</code> to see the users PUN, or <code>ps aux | grep -i nginx</code> to see all the PUNs. From the ondemand web UI theres an option to "Restart Web Server" which essentially kills and restarts the users PUN.</p>
2176+
<ol>
2177+
<li>/pun/sys/dashboard</li>
2178+
</ol>
2179+
<p>The dashboard is mostly covered in section 4, but just wanted to denote that apache then redirects us here after the PUN has been started where users can do everything else. At this step OOD will warn you about things like "Home Directory Not Found" and such. If you get this far I'd recommend you troubleshoot issues with users' home dir, NASii, and free space: <code>df | grep $HOME</code>, <code>du -sh $HOME</code>, <code>journalctl -u autofs</code>, and umount stuff. Check that <code>$HOME/ondemand</code> exists perhaps.</p>
2180+
<ol>
2181+
<li>OOD Apps</li>
2182+
</ol>
2183+
<p>When users start an app like JuyterLab or a VNC desktop the job is submitted by the users' PUN and here OOD copies and renders (with ERB) the global app template from <code>/var/www/ood/apps/sys/&lt;app_name&gt;/template/*</code> to <code>$HOME/ondemand/data/sys/dashboard/batch_connect/sys/&lt;app_name&gt;/(output)/&lt;session_id&gt;</code>. Any errors encountered at this step will be in <code>$HOME/ondemand/data/sys/dashboard/batch_connect/sys/&lt;app_name&gt;/(output)/&lt;session_id&gt;/*.log</code>.</p>
2184+
<ol>
2185+
<li>Misc</li>
21892186
</ol>
2187+
<p>Maybe the ondemand server is just in some invalid state and needs to be reset. I'd recommend you check the puppet conf at <code>/etc/puppetlabs/puppet/puppet.conf</code>, run <code>puppet agent -t</code> , and maybe restart the machine. Running puppet will force restart the apache server and regenerate OOD from the ood config yamls. Then you can restart the server by either ssh-ing to the server and running <code>reboot</code>, or by ssh-ing to proxmox and running <code>qm reset &lt;vmid&gt;</code> as root. TIP: you can find the vmid by finding the server in <code>qm list</code>. </p>
21902188
<h2 id="ood-fqdns">OOD FQDNs<a class="headerlink" href="#ood-fqdns" title="Permanent link">&para;</a></h2>
21912189
<h3 id="farm">Farm<a class="headerlink" href="#farm" title="Permanent link">&para;</a></h3>
21922190
<h4 id="production-ondemandfarmhpcucdavisedu">Production: <code>ondemand.farm.hpc.ucdavis.edu</code><a class="headerlink" href="#production-ondemandfarmhpcucdavisedu" title="Permanent link">&para;</a></h4>

pr-preview/pr-32/franklin/software/modules/index.html

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -3825,7 +3825,7 @@ <h3 id="corset">corset<a class="headerlink" href="#corset" title="Permanent link
38253825
<h3 id="ctffind">ctffind<a class="headerlink" href="#ctffind" title="Permanent link">&para;</a></h3>
38263826
<p>Fast and accurate defocus estimation from electron micrographs.</p>
38273827
<p><strong>Versions</strong>: 4.1.14</p>
3828-
<p><strong>Arches</strong>: intel, amd</p>
3828+
<p><strong>Arches</strong>: amd, intel</p>
38293829
<p><strong>Modules</strong>: <code>ctffind/4.1.14+intel</code>, <code>ctffind/4.1.14+amd</code></p>
38303830
<h3 id="cuda">cuda<a class="headerlink" href="#cuda" title="Permanent link">&para;</a></h3>
38313831
<p>CUDA is a parallel computing platform and programming model invented by
@@ -3897,7 +3897,7 @@ <h3 id="gatk">gatk<a class="headerlink" href="#gatk" title="Permanent link">&par
38973897
<h3 id="gcc">gcc<a class="headerlink" href="#gcc" title="Permanent link">&para;</a></h3>
38983898
<p>The GNU Compiler Collection includes front ends for C, C++, Objective-C,
38993899
Fortran, Ada, and Go, as well as libraries for these languages.</p>
3900-
<p><strong>Versions</strong>: 4.9.4, 5.5.0, 7.5.0</p>
3900+
<p><strong>Versions</strong>: 5.5.0, 4.9.4, 7.5.0</p>
39013901
<p><strong>Arches</strong>: generic</p>
39023902
<p><strong>Modules</strong>: <code>gcc/5.5.0</code>, <code>gcc/7.5.0</code>, <code>gcc/4.9.4</code></p>
39033903
<h3 id="gctf">gctf<a class="headerlink" href="#gctf" title="Permanent link">&para;</a></h3>
@@ -4207,7 +4207,7 @@ <h3 id="nextflow">nextflow<a class="headerlink" href="#nextflow" title="Permanen
42074207
<p><strong>Modules</strong>: <code>nextflow/22.10.1</code></p>
42084208
<h3 id="openjdk">openjdk<a class="headerlink" href="#openjdk" title="Permanent link">&para;</a></h3>
42094209
<p>The free and opensource java implementation</p>
4210-
<p><strong>Versions</strong>: 16.0.2, 11.0.17_8</p>
4210+
<p><strong>Versions</strong>: 11.0.17_8, 16.0.2</p>
42114211
<p><strong>Arches</strong>: generic</p>
42124212
<p><strong>Modules</strong>: <code>openjdk/11.0.17_8</code>, <code>openjdk/16.0.2</code></p>
42134213
<h3 id="openldap">openldap<a class="headerlink" href="#openldap" title="Permanent link">&para;</a></h3>
@@ -4354,9 +4354,9 @@ <h3 id="relion">relion<a class="headerlink" href="#relion" title="Permanent link
43544354
stand-alone computer program that employs an empirical Bayesian approach
43554355
to refinement of (multiple) 3D reconstructions or 2D class averages in
43564356
electron cryo-microscopy (cryo-EM).</p>
4357-
<p><strong>Versions</strong>: 4.0.1, 4.0.0, 3.1.3</p>
4357+
<p><strong>Versions</strong>: 3.1.3, 4.0.1, 4.0.0</p>
43584358
<p><strong>Variants</strong>: gpu, cpu</p>
4359-
<p><strong>Arches</strong>: intel+gpu_delay, intel, amd</p>
4359+
<p><strong>Arches</strong>: intel+gpu_delay, amd, intel</p>
43604360
<p><strong>Modules</strong>: <code>relion/cpu/3.1.3+amd</code>, <code>relion/gpu/3.1.3+amd</code>, <code>relion/gpu/3.1.3+intel</code>, <code>relion/cpu/4.0.0+amd</code>, <code>relion/gpu/4.0.0+amd</code>, <code>relion/gpu/4.0.0+intel</code>, <code>relion/3.1.3</code>, <code>relion/4.0.0</code>, <code>relion/cpu/4.0.1+amd</code>, <code>relion/gpu/4.0.1+amd</code>, <code>relion/4.0.1</code>, <code>relion/gpu/4.0.1+intel+gpu_delay</code>, <code>relion/gpu/4.0.1+intel</code></p>
43614361
<h3 id="relion-bbr">relion-bbr<a class="headerlink" href="#relion-bbr" title="Permanent link">&para;</a></h3>
43624362
<p>A modified version of Relion supporting block-based-reconstruction as
@@ -4367,7 +4367,7 @@ <h3 id="relion-bbr">relion-bbr<a class="headerlink" href="#relion-bbr" title="Pe
43674367
<p><strong>Modules</strong>: <code>relion-bbr/gpu/3.1.2+intel</code></p>
43684368
<h3 id="relion-helper">relion-helper<a class="headerlink" href="#relion-helper" title="Permanent link">&para;</a></h3>
43694369
<p>Utilities for Relion Cryo-EM data processing on clusters.</p>
4370-
<p><strong>Versions</strong>: 0.3, 0.2, 0.1</p>
4370+
<p><strong>Versions</strong>: 0.2, 0.1, 0.3</p>
43714371
<p><strong>Arches</strong>: generic</p>
43724372
<p><strong>Modules</strong>: <code>relion-helper/0.1</code>, <code>relion-helper/0.2</code>, <code>relion-helper/0.3</code></p>
43734373
<h3 id="repeatmasker">repeatmasker<a class="headerlink" href="#repeatmasker" title="Permanent link">&para;</a></h3>

pr-preview/pr-32/search/search_index.json

Lines changed: 1 addition & 1 deletion
Large diffs are not rendered by default.

0 commit comments

Comments
 (0)