[Beowulf] First cluster in 20 years - questions about today

[Jörg Saßmannshausen]

Hi Mark,

being a chemist and working in HPC for some years now, for a change I can make 
some contribution to the list as well.

I would not advice to use hardware which is over 5 years old, unless somebody 
else is footing the electricity bill. The new AMDs are much faster and also as 
you have more cores per node, you can run larger simulations without having 
InfiniBand interconnections. The next question would be which programs do you 
want to use? ORCA? NWChem? Gamess-US? CP2K/Castep? They all have different 
requirements and the list is by no means exhaustive. Do you just want to stick 
to DFT calculations or wavefunction ones as well (like CASSCF, CASPT2)? The 
bottom line is you want to have something which is efficient and tailored to the 
program(s) you want to use. 

Forget about Solaris. I don't know any code other than Gamess-US which is 
supporting Solaris. Stick to Linux. From what you said I guess you want to use 
code like CP2K which requires large memory. Again the latest AMD can address 
really large memory so I would suggest to go for that, if you really want to 
be productive. You might want to consider using NVMe as scratch/swap or even 
OS drive and, if you want to use CP2K, make sure you got enough memory and 
cores. 
If you just want to toy around then by all means use old hardware but you will 
have more frustration than fun.

For your information: I am a 'gentleman' scientist, i.e. I do my research, 
chemistry in my case, like most respectable scientist in the evening or 
weekend and I still got a daytime job to attend to. By enlarge I get one 
publication out per year in highly cited journals. Right now, as until 
recently I had some clusters at my disposal, I got an old 8 core box with 42 
GB or RAM which I am planning to replace this year with an AMD one for reasons 
already mentioned on the list. I wanted to do that last year but for one 
reason or another that did not work out. My desktop is a Intel(R) Core(TM) 
i7-4770 CPU @ 3.40GHz machine which also does calculations and post-
processing. My bottle neck right now is the time I need to write up stuff, 
another reason why I am still using the old server. At least it is heating my 
dining room. :-)

Let me know if you got any more questions, happy to help out a colleague!

All the best

Jörg

Am Samstag, 1. Februar 2020, 22:21:09 GMT schrieb Mark Kosmowski:
> 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).)
> 
> 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?
> 
> Will it be worthwhile to learn a cluster management software?  If so,
> suggestions?
> 
> 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?
> 
> 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?
> 
> Thank you all for still being here!