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I don’t see anything wrong in Jonathan’s advice. I’d also add that for computational chemistry, depending on model size and CPU, a gigabit network could be a bottleneck if you use a multi-node solver. I’ve seen bottlenecking on small models even with FDR Infiniband.
GPUs could also be useful for compatible solvers.
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<div><span style="-webkit-tap-highlight-color: rgba(0, 0, 0, 0);">(From </span><a href="https://its.tntech.edu/display/MON/HPC+Sample+Job%3A+NAMD">https://its.tntech.edu/display/MON/HPC+Sample+Job%3A+NAMD</a>)<span style="-webkit-tap-highlight-color: rgba(0, 0, 0, 0);"><br>
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<div>So heterogeneity may not be a problem if you stick with large-core OpenMP jobs. A scheduler like Slurm could be useful if you want to stack up a bunch of jobs in advance. Cluster management software might not be strictly required for a few-node single-user
cluster, but something like OpenHPC isn’t too hard to get running.</div>
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<div>If you were going to keep the old (2-core?) nodes around, I’d probably turn them into a storage cluster (Ceph, Gluster, etc). No idea if their power draw is too high to be worthwhile, though.<br>
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<div><span style="background-color: rgba(255, 255, 255, 0);">--</span></div>
<span style="background-color: rgba(255, 255, 255, 0);">Mike Renfro, PhD / HPC Systems Administrator, Information Technology Services<br>
<a href="tel:931%20372-3601" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="0/1" style="-webkit-text-decoration-color: rgba(0, 0, 0, 0.258824);">931 372-3601</a> / Tennessee Tech University</span></div>
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<blockquote type="cite">On Feb 1, 2020, at 9:21 PM, Mark Kosmowski <mark.kosmowski@gmail.com> wrote:<br>
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<div dir="auto">I've been out of computation for about 20 years since my master degree. I'm getting into the game again as a private individual. When I was active Opteron was just launched - I was an early adopter of amd64 because I needed the RAM (maybe
more accurately I needed to thoroughly thrash my swap drives). I never needed any cluster management software with my 3 node, dual socket, single core little baby Beowulf. (My planned domain is computational chemistry and I'm hoping to get to a point where
I can do ab initio catalyst surface reaction modeling of small molecules (not biomolecules).)
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<div dir="auto">I'm planning to add a few nodes and it will end up being fairly heterogenous. My initial plan is to add two or three multi-socket, multi-core nodes as well as a 48 port gigabit switch. How should I assess whether to have one big heterogenous
cluster vs. two smaller quasi-homogenous clusters?</div>
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<div dir="auto">Will it be worthwhile to learn a cluster management software? If so, suggestions?</div>
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<div dir="auto">Should I consider Solaris or illumos? I do plan on using ZFS, especially for the data node, but I want as much redundancy as I can get, since I'm going to be using used hardware. Will the fancy Solaris cluster tools be useful?</div>
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<div dir="auto">Also, once I get running, while I'm getting current with theory and software may I inquire here about taking on a small, low priority academic project to make sure the cluster side is working good?</div>
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<div dir="auto">Thank you all for still being here!</div>
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