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Building my own cluster :)

L

lollysticky

Weaksauce
Joined
Aug 23, 2008
Messages
65
Hi there,

I'm a bioinformatician looking to build a system to experiment and play with. It will run a Fedora 13 server 'minimal install' setup. I want a cluster of 3 nodes, and each node should be:

1) cost-effective (+ preferably low-budget) : I don't need high end CPUs
2) small: preferably mini-itx
3) no need for a graphics card... I will be running parallel programs on the cluster who do not profit from GPU power.
4) power-efficient CPU: low wattage


for each node, I was thinking along the lines of:
========== intel =========
Intel Celeron Dual Core E3300 (2 cores, 2.5Ghz, x86_64, 800Mhz FSB)
2Gig RAM
Intel Desktop Board DG41MJ
smallish SATA2 HD


Now, onto my questions:
1) does anyone in here have an idea or suggestion for another node composition? I tried to come up with a decent AMD alternative for about the same costs but I failed to do so.
2) how would I power the nodes? Three separate PSUs are over-the-top...
3) general advice :p


Thanks to anyone who would reply!
 
Will you be building your own case or something?

Prelim AMD setup:
$59 - AMD Athlon II X2 245 CPU
$55 - ZOTAC NF6100-E-E Nvidia nForce 430 MCP Mini ITX Motherboard
$44 - G.Skill 2GB DDR2 800 RAM
---
Total: $108 plus tax and shipping

Oh and three PSUs are more than likelt since there's no adapter I'm aware of that lets you have 3 x 24Pin connectors as well as 4Pin CPU connectors off one PSU.
 
I was thinking about using an 'open' setup :p simply use some bolts to distance the motherboards from each other (stacked on top of each other), and a small compartment below where the HDs would be positioned. Haven't figured out the PSU part since I don't know how to tackle that problem :)
 
Thats an awesome ideal.. I Think I may give it a shot with a 2nd atom d510 board in my server to increase the processing power, but keep it silent & power effecient.
 
Ditch the hard drive per node and netboot from a 'bootstrap' node that does have a hard drive. Unless of course your application requires it.

X3 435 is pretty cost effective considering it gets you a whole extra core which for the extra $10/node seems worth it. I don't like the lack of options for AMD MiniITX boards though, not really a fan of the nVidia chipsets, especially their truly shit NICs (which could be a big problem for a cluster), and I can't find an AMD chipset board at that size.
 
keenan said:
Ditch the hard drive per node and netboot from a 'bootstrap' node that does have a hard drive. Unless of course your application requires it.

X3 435 is pretty cost effective considering it gets you a whole extra core which for the extra $10/node seems worth it. I don't like the lack of options for AMD MiniITX boards though, not really a fan of the nVidia chipsets, especially their truly shit NICs (which could be a big problem for a cluster), and I can't find an AMD chipset board at that size.
Click to expand...

well idd... that is the biggest problem for the AMD setup
the zotac board seems the only low-cost solution, but f.e. the bios options of that board are absolutely minimal... and I too generally am not to found of nVidia chipsets; had some bad experiences with it :)


@keenan: never tried netboot. I'll look into it :)
 
DRBL is supposed to be a pretty good/easy way to do it. There's a fair amount of documentation out there on doing it manually too if you search for things like 'diskless linux cluster'.

Another, possibly easier, cost-saving option would be to boot from USB sticks or maybe even CD.
 
keenan said:
DRBL is supposed to be a pretty good/easy way to do it. There's a fair amount of documentation out there on doing it manually too if you search for things like 'diskless linux cluster'.

Another, possibly easier, cost-saving option would be to boot from USB sticks or maybe even CD.
Click to expand...

as far as I understand it, these things eat memory as well and the programs I will be running will utilize all the memory :p
I think the USB-boot might be a better solution for me
 
lollysticky said:
as far as I understand it, these things eat memory as well and the programs I will be running will utilize all the memory
Click to expand...
You can either mount the runtime filesystem as a small ramdisk (say 64MB or something) or mount it via NFS and not incur any memory penalty. NFS root is a bit trickier to set up, and obviously results in more network traffic.

Lots of options to choose from though, just trying to save some money and in the long run, time, especially if you ever decide to scale to more than a few nodes.
 
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