[Beowulf] Deskside clusters

[Michael H. Frese]

Jim,

I'm reluctant to expose my ignorance, but I think I have some experience 
to share.  And I don't believe this is a cluster issue.

My company -- and I do mean my company -- did 2-d multiphysics MHD 
simulations up until about 4 years ago using our proprietary multiblock 
domain decomposition code.  The diffusive magnetic field solver used all 
the vector operators in EM. So we share that much of the problems you 
are wanting to run.

At the end, we did our computations on 4 workstations connected by 
ancient single-channel Infiniband -- approximately 10 GB/sec but with ~1 
micro second latency which was critical for the small messages we were 
sending.

About 10 years ago Mellanox was dumping those and we bought 24 cards and 
two switches, one 8 port and one 16 port.  They cost us a little more 
than GB ethernet cards, but they were 30-40 times shorter latency.

So we built two clusters in 2012.  Both used handbuilt deskside 
workstation boxes which we set up on commercial retail store chrome 
racks -- NOT 1U or 2U.

As time went by, we upgraded to dual core, then quad core, then 8 core 
CPUs with motherboards and memory to match.  We used CentOS 5 for the 
Infiniband until it wasn't suitable for the motherboards required and 
then we went to CentOS 7.  We never paid for RHEL.

At the last version, we found that we often were able to run problems on 
single 8-core machines.

We stuck with AMD chips because they were faster for the money than 
Intel's.  The last CPUs we bought were capable of hyperthreading so we 
could run 16 jobs on each 8-core box.

I bet one deskside workstation running an AMD Ryzen 9 5900X 12-core CPU 
<https://www.google.com/search?client=firefox-b-1-d&q=amd+12+core> would 
be able to do the job you want, quietly, at low power, and hence low 
cooling requirement. Your problems seem to be embarrasingly parallel, 
but if you need communication between processes you could use in-memory 
communication, which is LOTS faster than any Infiniband.  And CentOS is 
fully equipped to get you an MPI with that.

Python is available.  Don't know about your NEC or plotting software.  
Source for NEC could be built on your new workstation if necessary.

You need a friendly sysadmin and programmer to set it up, get it going, 
and get you around the list of approved workstations.

Hope this isn't too far from your requirements.  Good luck!

Mike



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