Difference between revisions of "2021 Cluster Instruction"

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(Created page with "Category:Math compute cluster ==General Use Information== ===Logging In=== The clas-compute system uses (mostly) CentOS 7 and 8 operating system. At this time, the main...")
 
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'''This page is now obsolete. Please go to https://ccm-docs.readthedocs.io '''
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[[Category:Math compute cluster]]
 
[[Category:Math compute cluster]]
 +
:''Up to [[CCM]]''
 
==General Use Information==
 
==General Use Information==
  
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</code>
 
</code>
  
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===Hosts===
+
===Nodes===
−
 
+
To see a list of all nodes, use:
−
There are lots of hosts (servers) in our system and you can view all of them by typing <code>qhost</code> at the prompt.
 
−
 
 
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<p class="MsoNormal"><span
 
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style="font-size: 10pt; font-family: Consolas; color: black;">malingoj@math-compute:~$
 
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qhost</span></p>
 
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<p class="MsoNormal"><span
 
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style="font-size: 10pt; font-family: Consolas; color: black;">HOSTNAME&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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ARCH&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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NCPU NSOC NCOR NTHR&nbsp;
 
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LOAD&nbsp; MEMTOT&nbsp; MEMUSE&nbsp; SWAPTO&nbsp; SWAPUS</span></p>
 
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<p class="MsoNormal"><span
 
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style="font-size: 10pt; font-family: Consolas; color: black;">----------------------------------------------------------------------------------------------</span></p>
 
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<p class="MsoNormal"><span
 
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lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
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16&nbsp;&nbsp; 32&nbsp; 0.01&nbsp;
 
−
251.4G&nbsp;&nbsp;&nbsp;
 
−
2.2G&nbsp;&nbsp;&nbsp;
 
−
4.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">chem-xenon-c02&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.03&nbsp;
 
−
251.4G&nbsp;&nbsp;&nbsp;
 
−
2.1G&nbsp;&nbsp;&nbsp;
 
−
4.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
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<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">chem-xenon-c03&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
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16&nbsp;&nbsp; 32&nbsp; 7.90&nbsp;
 
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251.4G&nbsp;&nbsp;&nbsp;
 
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6.0G&nbsp;&nbsp;&nbsp;
 
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4.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
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<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">chem-xenon-c04&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32 14.95&nbsp;
 
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251.4G&nbsp;&nbsp;&nbsp; 8.2G&nbsp;&nbsp;&nbsp;
 
−
4.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">chem-xenon-c05&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.03&nbsp;
 
−
251.4G&nbsp;&nbsp;&nbsp;
 
−
2.1G&nbsp;&nbsp;&nbsp;
 
−
4.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">chem-xenon-c06&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.01&nbsp;
 
−
251.4G&nbsp;&nbsp;&nbsp;
 
−
2.3G&nbsp;&nbsp;&nbsp;
 
−
4.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">clas-pi-c01&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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lx-armhf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
4&nbsp;&nbsp;&nbsp;
 
−
1&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;
 
−
4&nbsp; 0.00&nbsp; 976.7M&nbsp;&nbsp;
 
−
61.4M&nbsp; 100.0M&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">clas-pi-c02&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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lx-armhf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
4&nbsp;&nbsp;&nbsp;
 
−
1&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;
 
−
4&nbsp; 0.00&nbsp; 976.7M&nbsp;&nbsp;
 
−
45.9M&nbsp; 100.0M&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c01&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.02&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c02&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.11&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c03&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;
 
−
&nbsp;&nbsp;32&nbsp;&nbsp;&nbsp;
 
−
2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c04&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c05&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c06&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.01&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c07&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c08&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c09&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c11&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c12&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.15&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c13&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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−
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<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c22&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c23&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;&nbsp;
 
−
62.9G&nbsp;&nbsp;&nbsp; 1.4G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-c24&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
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-&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;-</span></p>
 
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<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-colibri-i01&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
64&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;
 
−
32&nbsp;&nbsp; 64&nbsp; 3.00
 
−
1007.9G&nbsp;&nbsp;&nbsp; 8.0G&nbsp;
 
−
932.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-compgen-c01&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
4&nbsp;&nbsp;&nbsp;
 
−
1&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;
 
−
4&nbsp; 0.00&nbsp;&nbsp;&nbsp;
 
−
3.7G&nbsp; 495.6M&nbsp;&nbsp;
 
−
34.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-compgen-c02&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
4&nbsp;&nbsp;&nbsp;
 
−
1&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;
 
−
4&nbsp; 0.00&nbsp;&nbsp;&nbsp;
 
−
3.7G&nbsp; 497.2M&nbsp;&nbsp;
 
−
34.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-compgen-c03&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
4&nbsp;&nbsp;&nbsp;
 
−
1&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;
 
−
4&nbsp; 0.00&nbsp;&nbsp;&nbsp;
 
−
3.7G&nbsp; 489.7M&nbsp;&nbsp;
 
−
34.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-compgen-c04&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
4&nbsp;&nbsp;&nbsp;
 
−
1&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;
 
−
4&nbsp; 0.00&nbsp;&nbsp;&nbsp;
 
−
3.7G&nbsp; 496.4M&nbsp;&nbsp;
 
−
34.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c01&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 948.4M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c02&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 953.5M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c03&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;
 
−
&nbsp;&nbsp;24&nbsp;&nbsp;&nbsp;
 
−
2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 954.2M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c04&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 941.8M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c05&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 946.8M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c06&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 942.1M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c07&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp;&nbsp;&nbsp;
 
−
1.0G&nbsp;&nbsp; 50.0G&nbsp;&nbsp;&nbsp;&nbsp;
 
−
0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c08&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 958.7M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c09&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 844.3M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 862.1M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c11&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.01&nbsp;&nbsp;
 
−
23.5G&nbsp; 939.4M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-c12&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
23.5G&nbsp; 844.9M&nbsp;&nbsp;
 
−
50.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-i01&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
24&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
12&nbsp;&nbsp; 24&nbsp; 0.00&nbsp;&nbsp;
 
−
94.4G&nbsp;&nbsp;&nbsp; 1.0G&nbsp;
 
−
178.3G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-gross-i02&nbsp;
 
−
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lx-amd64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
32&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;
 
−
16&nbsp;&nbsp; 32&nbsp; 0.00&nbsp;
 
−
377.9G&nbsp;&nbsp;&nbsp; 1.1G&nbsp;
 
−
130.0G&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span></p>
 
−
<p class="MsoNormal"><span
 
−
style="font-size: 10pt; font-family: Consolas; color: black;">math-turing&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp; -&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
−
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
 
−
</span></p>
 
−
 
 
−
 
 
−
As far as columns go:
 
−
 
 
−
 
 
−
NCPU is the number of logical CPUs
 
−
 
 
−
NSOC is the number of physical CPUs sockets
 
−
 
 
−
NCOR is the number of physical cores
 
−
 
 
−
NTHR is the number of threads
 
−
 
 
−
LOAD is the /100 load of the server
 
−
 
 
−
MEMTOT is the total physical memory
 
−
 
 
−
MEMUSE is the total physical memory used
 
−
 
 
−
SWAPTO is the total swap memory
 
−
 
 
−
SWAPUS is the total swap memory used
 
−
 
 
  
−
There are pros and cons of using more threads than physical cores (aka hyperthreading) and in some cases it helps and some it doesn’t. In general, it helps if you’re running a large multithreaded job on one machine, but slows things down if you’re using MPI or running a bunch of small single core jobs. For our purposes and limited budget, it’s usually hyperthreading enabled. Colibri is the main exception as it’s the main cluster for MPI jobs. math-colibri queue will only assign 16 slots per node even though it has 32 threads per node/host/server. When colibri is idle, we can enable colibri hosts into math-all and it will use all 32 threads. Easy answer? Just use math-all.
+
<pre>
 +
[jmandel@clas-compute ~]$ sinfo -N
 +
NODELIST          NODES        PARTITION STATE
 +
chem-xenon-c01        1        chem-xenon unk* 
 +
chem-xenon-c02        1        chem-xenon unk* 
 +
chem-xenon-c03        1        chem-xenon unk* 
 +
chem-xenon-c04        1        chem-xenon unk* 
 +
chem-xenon-c05        1        chem-xenon unk* 
 +
chem-xenon-c06        1        chem-xenon unk* 
 +
clas-rcdesktop-01      1    clas-rcdesktop down*
 +
math-alderaan-c01      1    math-alderaan alloc
 +
math-alderaan-c02      1    math-alderaan alloc
 +
math-alderaan-c03      1    math-alderaan alloc
 +
math-alderaan-c04      1    math-alderaan alloc
 +
math-alderaan-c05      1    math-alderaan alloc
 +
math-alderaan-c06      1    math-alderaan alloc
 +
math-alderaan-c07      1    math-alderaan alloc
 +
math-alderaan-c08      1    math-alderaan alloc
 +
math-alderaan-c09      1    math-alderaan alloc
 +
math-alderaan-c10      1    math-alderaan alloc
 +
math-alderaan-c11      1    math-alderaan alloc
 +
math-alderaan-c12      1    math-alderaan alloc
 +
math-alderaan-c13      1    math-alderaan alloc
 +
math-alderaan-c14      1    math-alderaan alloc
 +
math-alderaan-c15      1    math-alderaan alloc
 +
math-alderaan-c16      1    math-alderaan mix 
 +
math-alderaan-c17      1    math-alderaan idle 
 +
math-alderaan-c18      1    math-alderaan idle 
 +
math-alderaan-c19      1    math-alderaan idle 
 +
math-alderaan-c20      1    math-alderaan idle 
 +
math-alderaan-c21      1    math-alderaan idle 
 +
math-alderaan-c22      1    math-alderaan idle 
 +
math-alderaan-c23      1    math-alderaan idle 
 +
math-alderaan-c24      1    math-alderaan idle 
 +
math-alderaan-c25      1    math-alderaan idle 
 +
math-alderaan-c26      1    math-alderaan idle 
 +
math-alderaan-c27      1    math-alderaan idle 
 +
math-alderaan-c28      1    math-alderaan idle 
 +
math-alderaan-c29      1    math-alderaan idle 
 +
math-alderaan-c30      1    math-alderaan idle 
 +
math-alderaan-c31      1    math-alderaan idle 
 +
math-alderaan-c32      1    math-alderaan idle 
 +
math-alderaan-h01      1 math-alderaan-gpu idle 
 +
math-alderaan-h02      1 math-alderaan-gpu idle 
 +
math-colibri-c01      1  math-colibri-gpu idle 
 +
math-colibri-c02      1  math-colibri-gpu idle 
 +
math-colibri-c03      1  math-colibri-gpu idle 
 +
math-colibri-c04      1  math-colibri-gpu unk* 
 +
math-colibri-c05      1  math-colibri-gpu unk* 
 +
math-colibri-c06      1  math-colibri-gpu unk* 
 +
math-colibri-c07      1  math-colibri-gpu unk* 
 +
math-colibri-c08      1  math-colibri-gpu unk* 
 +
math-colibri-c09      1  math-colibri-gpu unk* 
 +
math-colibri-c10      1  math-colibri-gpu unk* 
 +
math-colibri-c11      1  math-colibri-gpu unk* 
 +
math-colibri-c12      1  math-colibri-gpu unk* 
 +
math-colibri-c13      1  math-colibri-gpu idle 
 +
math-colibri-c14      1  math-colibri-gpu idle 
 +
math-colibri-c15      1  math-colibri-gpu idle 
 +
math-colibri-c16      1  math-colibri-gpu idle 
 +
math-colibri-c17      1  math-colibri-gpu idle 
 +
math-colibri-c18      1  math-colibri-gpu idle 
 +
math-colibri-c19      1  math-colibri-gpu idle 
 +
math-colibri-c20      1  math-colibri-gpu idle 
 +
math-colibri-c21      1  math-colibri-gpu idle 
 +
math-colibri-c22      1  math-colibri-gpu idle 
 +
math-colibri-c23      1  math-colibri-gpu idle
 +
math-colibri-c24      1  math-colibri-gpu idle 
 +
math-score-c01        1        math-score unk* 
 +
math-score-c02        1        math-score unk* 
 +
math-score-c03        1        math-score idle 
 +
math-score-c04        1        math-score idle 
 +
math-score-c05        1        math-score idle 
 +
</pre>
  
−
Swap memory is both a blessing and a curse. It’s basically using a slow hard drive (or array of hard drives) for extra memory. While this allows your job to continue to run without blowing up and failing, the CPU has to wait to snag data from that swap so things usually drop to a crawl if you start ‘swapping’. If something is taking forever and you ‘qhost’ and see it at full memory and into swap, let Joe know so he can try to fix it without killing your jobs.
 
  
−
It looks confusing but there is a method to the madness in the naming convention. Obviously, math-colibri and math-gross is the identifier for what cluster/building the servers are in, but the –c## and –i## stand for compute and interactive. the c## servers are usually part of the queuing system and the i## ones are for interactive use.
+
It looks confusing but there is a method to the madness in the naming convention. Obviously, math-colibri and math-score are the identifiers for what cluster/building the servers are in, but the –c## and –i## stand for compute and interactive. the c## servers are usually part of the queuing system and the i## ones are for interactive use. Again, never ssh to compute nodes directly.
  
 
==Scheduler Instructions==
 
==Scheduler Instructions==
Line 542: Line 161:
 
===Submitting a job===
 
===Submitting a job===
  
−
The <code>qsub</code> command is used to submit a job into a queue. Your job should be a script that is accessible to the compute nodes. There are several switches you can add to the qsub command to set the submission options - the most common ones are:
+
The <code>sbatch</code> command is used to submit a job into a queue. Your job should be a script that is accessible to the compute nodes. You can add switches to the <code>sbatch</code> command, but it is recommended to make them a part of your batch script. Here is a sample SLURM batch script: COMING SOON
−
 
 
−
<table class="MsoNormalTable" style="width: 547.5pt;"
 
−
border="1" cellpadding="0" width="0">
 
−
  <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-q
 
−
[queuename]</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">Submit
 
−
the job into a certain queue (you should almost always do this)</span></p>
 
−
      </td>
 
−
    </tr>
 
−
    <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-pe
 
−
[parallel environment]&nbsp;&nbsp;</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">Submit
 
−
the job with a specified parallel environment</span></p>
 
−
      </td>
 
−
    </tr>
 
−
</table>
 
−
 
 
−
By default, a job will run with one "slot" (aka core reservation). If your job is going to use more than one CPU core, use the -pe smp XX where XX is the number of cores your job will consume. (16 in the example below)
 
−
 
 
−
Example:
 
−
 
 
−
<code>qsub -q math-all -pe smp 16 ./awesomescript.sh</code>
 
  
 
===Viewing queues and job status===
 
===Viewing queues and job status===
  
−
The <code>qstat</code> and <code>qhost</code> command are used to gather information from the scheduler. Some of the most common switches are:
+
The <code>squeue</code> command is used to gather information from the scheduler. Some of the most common switches are: COMING SOON
−
 
 
−
<table class="MsoNormalTable" style="width: 552pt;"
 
−
border="1" cellpadding="0" width="0">
 
−
    <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-q
 
−
[queuename]</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">Request
 
−
information on a certain queue. If you don't specify this option, all
 
−
queues will be given</span></p>
 
−
      </td>
 
−
    </tr>
 
−
    <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-f</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">Request
 
−
full output - this is similar to giving a verbose output</span></p>
 
−
      </td>
 
−
    </tr>
 
−
    <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-u
 
−
[username]</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">Request
 
−
list of jobs for a certain user. Use -u '*' to show all users.</span></p>
 
−
      </td>
 
−
    </tr>
 
−
    <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-j
 
−
[jobid]</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">Request
 
−
information on a job. This is useful if your job throws an E (error)
 
−
code.</span></p>
 
−
      </td>
 
−
    </tr>
 
−
    <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-g
 
−
c</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">Show
 
−
status for all available queues - shows the used and available
 
−
resources.</span></p>
 
−
      </td>
 
−
    </tr>
 
−
</table>
 
−
 
 
−
 
 
−
The command <code>qhost</code> will show information on each server managed by the scheduler - mainly number of CPUs/Threads, total memory and total memory used, and total swap memory space and swap memory space used.
 
−
 
 
−
===Modifying Jobs===
 
−
 
 
−
The <code>qmod</code> and <code>qalter</code> commands are used to modify job settings or statuses.
 
−
 
 
−
The common <code>qmod</code> commands are:
 
−
 
 
−
<table class="MsoNormalTable" style="width: 553.5pt;"
 
−
border="1" cellpadding="0" width="0">
 
−
    <tr style="">
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">-sj
 
−
[jobid]</span></p>
 
−
      </td>
 
−
      <td style="padding: 1.5pt;">
 
−
      <p class="MsoNormal"><span
 
−
style="font-size: 11pt; font-family: &quot;Times New Roman&quot;,serif; color: black;">suspend
 
−
(pause) a job</span></p>
 
−
      </td>
 
−
    </tr>
 
−
    <tr style="">
 
−
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      <p class="MsoNormal"><span
 
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(unpause) a job</span></p>
 
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a job (restart and submit back in queue)</span></p>
 
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[jobid]</span></p>
 
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job error state of a job</span></p>
 
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The common <code>qalter</code> commands are:
 
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[queuename]</span></p>
 
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      <p class="MsoNormal"><span
 
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the job queue to the specified queue</span></p>
 
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[parallelenvironment] [slots]</span></p>
 
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the parallel environment and/or number of slots used for the job</span></p>
 
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</table>
 

Latest revision as of 02:29, 15 November 2021

This page is now obsolete. Please go to https://ccm-docs.readthedocs.io

Up to CCM

General Use Information

Logging In

The clas-compute system uses (mostly) CentOS 7 and 8 operating system. At this time, the main way of using the system is to use an SSH client to login to a terminal session on clas-compute. You will need to be on the CU Denver network (wired or CU Denver wireless, not CU Denver Guest), or using the university's VPN client.

This system uses your normal portal/email username and password.

On Windows, you will need an SSH client. There are several out there, but generally most people use PuTTY which is available for download here. You can use either 32 or 64 bit versions - computers that require the 32 bit version are rather rare (early Windows 7/Vista/XP). The Host Name is clas-compute.ucdenver.pvt. (image is from the old system, but same difference)

PuTTY Windows

You can also use the Windows 10 subsystem for Linux, where you install a Linux distribution as an app and can use it to ssh out like from a terminal window on any Linux machine. This is often more stable than Putty, which tends to get stuck on some computers.

On Macintosh, you can either use a specialized SSH client or Terminal which is built into the operating system. While in Finder on your Mac, press the Option, Shift, and U keys simultaneously. The Utilities folder should appear and the Terminal is within this folder. Open terminal and at the prompt type in:

ssh awesomeperson@clas-compute.ucdenver.pvt

Whereas awesomeperson would be your UCD username. After connecting, it should ask for your UCD password and enter it at this point.

Science will then occur and you should be at the clas-compute prompt and in your home directory.

Interactive Use

Using a server ‘interactively’ (aka not scheduling a job) is often needed for troubleshooting a job or just watching what it is doing in real time. After SSH’ing into math-compute, you can type ssh math-colibri-i01 or whatever server you want to go directly to the server. Please do not run anything directly on compute nodes, which are reserved for jobs under the control of the scheduler, even if you may be able to ssh there. These are nodes with names like math-colibri-c01 with the "c" before the number. Using compute nodes, where other people run jobs through the scheduler, will interfere with their work and make you very unpopular.


Using ‘screen’ is generally a good idea both math-compute or the interactive nodes. Basically was screen does is starts a virtual terminal inside your terminal. Sound confusing? It is. The plus of this virtual terminal is if you get disconnected, whatever you were running is still going.

screen –S ‘bananaphone’ (make the name whatever you want) creates a new terminal with that name

If you want to disconnect from the screen but leave it running, hit the combination of Control-A and press the D key to disconnect. Control-A is the combo to let screen know you want to do an action.

When you want to reconnect to the screen later, log back onto wherever you started the screen and type screen –r. If you have more than one screen, it’ll complain and tell you the screens you have available to reconnect to. screen –r ‘bananaphone’ to reconnect to that screen. Sometimes there is a number in front of the screen so screen –r 3128.bananaphone. It’ll tell you the number in the screen –r info screen.

File Storage

Math home directories are on a shared server with 40TB total (right now). Projects are found in /storage/department/projects (where department may be one of many departments who use this system).

For example, the mixtures project is in /storage/math/projects/mixtures.

If you need a lot of data storage, please contact Joe before filling everything you can find.

df –h will show you the storage arrays and how much space is available. There are different types of ‘empty’ space in linux so it may say there is plenty of space in df –h yet the array is full.

Passwords

The system uses your normal UCD portal/email logon username and password. Users must be approved before using the system, so if your login is not working, you probably are not on the approved/initialized list yet.

Requesting information about the environment

Queues

There are queues for different departments on math-compute because it points to a central scheduler for all of CLAS. To see these queues type sinfo:

PARTITION AVAIL TIMELIMIT NODES STATE NODELIST

math-alderaan up 4-00:00:00 32 down* math-alderaan-c[01-32]

math-alderaan-gpu up 4-00:00:00 1 down* math-alderaan-h01

math-alderaan-gpu up 4-00:00:00 1 unk* math-alderaan-h02

math-colibri-gpu up infinite 12 unk* math-colibri-c[01-02,04-12,23]

math-colibri-gpu up infinite 12 idle math-colibri-c[03,13-22,24]

math-score up infinite 5 unk* math-score-c[01-05]

chem-xenon up infinite 6 unk* chem-xenon-c[01-06]

Nodes

To see a list of all nodes, use: 

[jmandel@clas-compute ~]$ sinfo -N
NODELIST           NODES         PARTITION STATE 
chem-xenon-c01         1        chem-xenon unk*  
chem-xenon-c02         1        chem-xenon unk*  
chem-xenon-c03         1        chem-xenon unk*  
chem-xenon-c04         1        chem-xenon unk*  
chem-xenon-c05         1        chem-xenon unk*  
chem-xenon-c06         1        chem-xenon unk*  
clas-rcdesktop-01      1    clas-rcdesktop down* 
math-alderaan-c01      1     math-alderaan alloc 
math-alderaan-c02      1     math-alderaan alloc 
math-alderaan-c03      1     math-alderaan alloc 
math-alderaan-c04      1     math-alderaan alloc 
math-alderaan-c05      1     math-alderaan alloc 
math-alderaan-c06      1     math-alderaan alloc 
math-alderaan-c07      1     math-alderaan alloc 
math-alderaan-c08      1     math-alderaan alloc 
math-alderaan-c09      1     math-alderaan alloc 
math-alderaan-c10      1     math-alderaan alloc 
math-alderaan-c11      1     math-alderaan alloc 
math-alderaan-c12      1     math-alderaan alloc 
math-alderaan-c13      1     math-alderaan alloc 
math-alderaan-c14      1     math-alderaan alloc 
math-alderaan-c15      1     math-alderaan alloc 
math-alderaan-c16      1     math-alderaan mix   
math-alderaan-c17      1     math-alderaan idle  
math-alderaan-c18      1     math-alderaan idle  
math-alderaan-c19      1     math-alderaan idle  
math-alderaan-c20      1     math-alderaan idle  
math-alderaan-c21      1     math-alderaan idle  
math-alderaan-c22      1     math-alderaan idle  
math-alderaan-c23      1     math-alderaan idle  
math-alderaan-c24      1     math-alderaan idle  
math-alderaan-c25      1     math-alderaan idle  
math-alderaan-c26      1     math-alderaan idle  
math-alderaan-c27      1     math-alderaan idle  
math-alderaan-c28      1     math-alderaan idle  
math-alderaan-c29      1     math-alderaan idle  
math-alderaan-c30      1     math-alderaan idle  
math-alderaan-c31      1     math-alderaan idle  
math-alderaan-c32      1     math-alderaan idle  
math-alderaan-h01      1 math-alderaan-gpu idle  
math-alderaan-h02      1 math-alderaan-gpu idle  
math-colibri-c01       1  math-colibri-gpu idle  
math-colibri-c02       1  math-colibri-gpu idle  
math-colibri-c03       1  math-colibri-gpu idle  
math-colibri-c04       1  math-colibri-gpu unk*  
math-colibri-c05       1  math-colibri-gpu unk*  
math-colibri-c06       1  math-colibri-gpu unk*  
math-colibri-c07       1  math-colibri-gpu unk*  
math-colibri-c08       1  math-colibri-gpu unk*  
math-colibri-c09       1  math-colibri-gpu unk*  
math-colibri-c10       1  math-colibri-gpu unk*  
math-colibri-c11       1  math-colibri-gpu unk*  
math-colibri-c12       1  math-colibri-gpu unk*  
math-colibri-c13       1  math-colibri-gpu idle  
math-colibri-c14       1  math-colibri-gpu idle  
math-colibri-c15       1  math-colibri-gpu idle  
math-colibri-c16       1  math-colibri-gpu idle  
math-colibri-c17       1  math-colibri-gpu idle  
math-colibri-c18       1  math-colibri-gpu idle  
math-colibri-c19       1  math-colibri-gpu idle  
math-colibri-c20       1  math-colibri-gpu idle  
math-colibri-c21       1  math-colibri-gpu idle  
math-colibri-c22       1  math-colibri-gpu idle  
math-colibri-c23       1  math-colibri-gpu idle  
math-colibri-c24       1  math-colibri-gpu idle  
math-score-c01         1        math-score unk*  
math-score-c02         1        math-score unk*  
math-score-c03         1        math-score idle  
math-score-c04         1        math-score idle  
math-score-c05         1        math-score idle


It looks confusing but there is a method to the madness in the naming convention. Obviously, math-colibri and math-score are the identifiers for what cluster/building the servers are in, but the –c## and –i## stand for compute and interactive. the c## servers are usually part of the queuing system and the i## ones are for interactive use. Again, never ssh to compute nodes directly.

Scheduler Instructions

Submitting a job

The sbatch command is used to submit a job into a queue. Your job should be a script that is accessible to the compute nodes. You can add switches to the sbatch command, but it is recommended to make them a part of your batch script. Here is a sample SLURM batch script: COMING SOON

Viewing queues and job status

The squeue command is used to gather information from the scheduler. Some of the most common switches are: COMING SOON

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