Computational Node Build: Please Critique

[Phew]

We are expanding our computational fluid dynamics (CFD) cluster at work, so I will be ordering four of these nodes. They need to offer reliability (since they will be at 100% load 24/7) and the most computational power per dollar possible. I will not be doing any overclocking. The machines will have Gentoo Linux installed and will be interfaced using Gigabit Ethernet. They need to have integrated video for occasional debugging.

I've been out of the hardware loop for a few years, but this is the best I could come up with after minimal research. Please let me know if there are any incompatability issues or if there are any better options for a given component. Micro-ATX is the form factor of choice due to space constraints. I have no AMD/Intel loyalties; our last build was AMD, but it looks like Intel has better offerings right now. The overall per-node budget is $500 shipped.


Intel Core 2 Duo E6550 Conroe 2.33GHz LGA 775 Processor Model BX80557E6550 - Retail
$178.99

ASUS P5L-MX LGA 775 Intel 945G Micro ATX Intel Motherboard - Retail
$74.99

CORSAIR ValueSelect 2GB (2 x 1GB) 240-Pin DDR2 SDRAM DDR2 667 (PC2 5300) Desktop
$75.99

Athenatech A3603BB.400 Black Steel MicroATX Mini Tower Computer Case 400W Power
$39.99

Western Digital Caviar SE WD800JD 80GB 7200 RPM SATA 3.0Gb/s Hard Drive - OEM
$42.99

Intel PWLA8391GTL 10/ 100/ 1000Mbps PCI Low Profile Desktop Network Adapter - OEM
$29.90-We have to use this NIC for Linux compatability reasons

LITE-ON Black IDE CD-ROM Drive Model LH-52N1P-185 - OEM
$12.99

TOTAL: $483.86 shipped

Thanks

 

[GenHoth]

It looks pretty good, though I'd recommend a quad core. Here is a thread about cheep quads. You should post your build there too. (Modified with a quad of course )

http://forums.anandtech.com/me...erthread=y&STARTPAGE=7

 

[Phew]

Thanks Hoth. Here is a Quad-core version:

Intel Core 2 Quad Q6600 Kentsfield 2.4GHz LGA 775 Processor Model BX80562Q6600
$294.99

ASUS P5B-VM SE LGA 775 Intel G965 Express uATX Intel Motherboard - Retail
$99.99

Patriot 2GB (2 x 1GB) 240-Pin DDR2 SDRAM DDR2 800 (PC2 6400) Dual Channel Kit
$88.99

Athenatech A3603BB.400 Black Steel MicroATX Mini Tower Computer Case 400W
$39.99

Western Digital Caviar SE WD800JD 80GB 7200 RPM SATA 3.0Gb/s Hard Drive - OEM
$42.99

LITE-ON Black IDE CD-ROM Drive Model LH-52N1P-185 - OEM
$12.99

Intel PWLA8391GTL 10/ 100/ 1000Mbps PCI Low Profile Desktop Network Adapter -
$29.99

TOTAL: $609.93+Shipping

 

[imported_shader]

how does your application work? just constant calculation? ever need to use up alot of ram (large datasets)? if not, might want to use only 1gb (just to be cheap).

also you probably wouldn't notice a 'real world' difference in using a cheaper processor (e4400) and save money.

it might help to know more about how the application works. and i'm also assuming it would be pretty much the only thing running on these computers.

after viewing some benchies at tomshardware.com it looks like the quad will probably double the performance of either one of these chips, but at more than twice the cost of the e4400. as far as value per dollar, probably much better off with e4400 (i compared e4300, e6420, and q6600).

e4400 - best value
e6550 - 4mb cache might help, but also might not be noticable for $50 more
q6600 - great performance, but high price (300 vs 175 vs 113)

i would probably stick with the 2gb ram and get the e4400.

 

[xitshsif]

Do you need the dedicated network card?

Also, DDR2-800 won't show any gains over DDR2 667 when running at stock FSB. It'll save you a couple bucks by sticking with DDR2 667.

 

[Knavish]

Why not junk the CDROM and install from a USB stick? Or just order one with the CD, install normally, and copy the HD image onto the others. (using the "dd" command in linux, for instance).

You could have all the nodes network boot (dhcp + bootp) from a single master, though this is probably more trouble than it's worth for a small cluster. This does make it much easier to add nodes, though, since all you have to do is edit a few configuration files on the master. I did this with a 30 node system & thought it was pretty fun to learn how to make all the network boot stuff work.

-Knavish

 

[Phew]

Thanks for the comments/suggestions. After looking at some benchmarks, it looks like Quad core offers very good performance gains for CFD applications, until the cell count gets so large that you are bottlenecking the memory bus.

Good call on the USB flash drive installation and slower memory. We did network boot for a year or so, it was a total disaster, so we keep it simple now. We've had problems with on-board NICs in the past, I guess we could try it first without the dedicated NIC.

Is that 400W power supply enough to power the quad core processor? We won't be powering a video card or any peripherals.

With your suggestions I'm down to $550+shipping for the Quad-core node.

Thanks again for the comments

 

[xitshsif]

400W isn't what I'd be concerned about. It's the fact that it's a cheap-o "come with the case" style one. In my experience they're not that reliable.

 

[Knavish]

Originally posted by: Phew
We've had problems with on-board NICs in the past, I guess we could try it first without the dedicated NIC.

The only problems I've had with an onboard NIC in linux were with an NVIDIA chipset before linux people developed support for it. Now I'm running gentoo on my desktop at home on a nvidia motherboard with no problems. What kind of motherboard are you looking at now? I'd be somewhat surprised if the integrated NIC didn't work out of the box.

Remember with quad core, if you want 1 GB of ram per CPU you'll need 4GB. If you're running 4GB you'll want to use the 64 bit version of linux to avoid the ~3.2 GB memory limit. Does your software work on 64 bit linux?

-Knavish

 

[Phew]

What kind of motherboard are you looking at now?

ASUS P5B-VM SE LGA 775 Intel G965 Express uATX Intel Motherboard - Retail

If you're running 4GB you'll want to use the 64 bit version of linux to avoid the ~3.2 GB memory limit. Does your software work on 64 bit linux?

We're just going to do 2x1 GB with the quad core processor, since we are still using a 32-bit Linux distribution.

 

[cmbehan]

Perhaps you should consider Intel boards...

You might want to consider something like

Intel BLKDP35DPM LGA 775 Intel P35 ATX Intel Motherboard - Retail
$106.99

and a larger ATX case....

With this you'll get better airflow in a full ATX case as well as a built-in Intel NIC.

I also think that (at stock speeds) Intel boards are as stable as they come.

 

[cmbehan]

Sorry...my suggestion didn't have on-board video.

Maybe this one would work:

Intel BLKDG33BUC LGA 775 Intel G33 Micro ATX Intel Motherboard - Retail
$102.99

 

[xitshsif]

I don't think an Intel board would offer much that the ASUS wouldn't. If you're thinking about ways to up reliability, switching out that PSU would be the first thing on my list.

 

[Knavish]

Originally posted by: Phew
We're just going to do 2x1 GB with the quad core processor, since we are still using a 32-bit Linux distribution.

So your CFD program needs less than 512 MB per process? I guess if you needed huge amounts of memory per process things might run slowly because you'd have too many elements to be simulated on a single CPU?

 

[Operandi]

Originally posted by: xitshsif
I don't think an Intel board would offer much that the ASUS wouldn't. If you're thinking about ways to up reliability, switching out that PSU would be the first thing on my list.

Agreed, if reliability is at all a concern that PSU has to go.

You don't need a ton of power for such a setup either. This 300 FSP would be an excellent choice for it's high efficiency, strong 12v rail, AFPC, and build quality.

 

[Phew]

I hear ya on the PSU. We built 4 nodes using a case+cheapo PSU from the same company over a year ago, and so far we have a 25% PSU failure rate. We'll probably just replace the PSUs as they go, and hope they don't take the mobo with them when they go.

The particular application we are running isn't really all that memory hungry. Only about 3 million cells in the CFD grid, which isn't very big. We just need to run hundreds of cases sequentially.

 

[lookouthere]

well, why you want to have hassle of changing failure psu when you buy 1 reliable psu and use it till you retire that comp