[Beowulf] A cluster for material simulation

Guillaume MICHAL gmichal at uow.edu.au
Mon Dec 3 15:20:26 PST 2007

Good morning all,
Our faculty is thinking about a cluster for material simulations. At the  
moment we would like to use FEM, MD, MPM and maybe in some cases a  
multiscale FEM/MD or MPM/MD. We will start with a very small cluster  
around 5 nodes to be familliar with this kind of system and then extend it  
to around 20 nodes. Tasks size could vary between 1G to let say 10G. FEM  
will use Abaqus or CODE_ASTER. I don't really know the name of the  
softwares for MPM and MD.
I did some reasearch and reading (by the way, Building clustered linux  
systems by Robert W.Lucke is a bit scary!) and defined 2 kind of systems.  
I'd like your opinion on these.

Both systems use a Gigabit ethernet, 2GB of memory per CPU, 80GB of sata  
hard drive per nodes.
Dekstop motherboard based system:
1 asus P5E WS Professional motherboard, 1066FSB, DDR2 800 NON ECC  
unbuffered, 2GigE ports, 1 Intel Q6600 CPU @2.4GHz 8MB L2 cache

Server motherboard based system:
Supermicroserver 6015C-MTB 1333/1066FSB, DDR2 667 ECC FB-DIMM, 2GigE  
ports, 2 intel Xeon 5410 CPU @2.3Ghz 12MB L2 cache

It might seems I'm comparing apples and oranges but theoretical peak  
performance is equivalent and in term of cost/CPU there is not a huge  
difference(150 to 250 A$), also the server solution use twice as less  
nodes wich could be interesting in term of space, cables, switch... For  
recycling the desktop option seems better except if we use the servers for  
some kind of graphic cluster in the futur.

Now the real questions:
	1- If I understood properly FEM is kind of memory bounded so DDR2  
800/1066FSB/8MB L2 cache or DDR2 667/1333FSB/12MB L2 cache -> kind of  
newbie to theses things!
	2- Which one seems better in term of performance, reliability?
	3- Do I need a distinct network for NFS sharing (thath's why I wanted 2  
GigE ports per nodes) or I put the shared data on the master node(Quote  
 from R.W.Luke book: "This is bad, bad, bad")?
	4- there is also the supermicro superserver 6015tw-tb with two dual  
socket motherboard in a 1U form factor (node it's just two nodes put in  
one box, no interconnections whatsoever apart from the PSU) with roughtly  
the same price per CPU compare to the other supermicro solution, could be  
interesting for an even more compact system, do you have any knowledge  
about this system?
	5- anything I didn't think of and might be worth checking such as "Oh!  
you need a fast hard drive as i/o is critical...;-)"

Thank you for your advices!
Guillaume Michal

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