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Dual (Nehalem) Xeon workstation <$2500

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May 10, 2009 3:37:35 AM

Hello,

I'm trying to build a Dual Xeon system for use as a data analysis workstation. I do some graphics work, so I need a decent graphics card. But, the main need for the heavy-duty horsepower and RAM is my data analysis work; I use Matlab (on Vista x64) for analyzing enormous data sets (i.e., neurophysiological [EEG] recordings). I need a system that is computationally fast and able to handle multiple demanding threads simultaneously.

I have about $2500 (max) to spend. This is my first complete system build, but I have a good deal of experience upgrading individual components. I am hoping to purchase a system in about 4 weeks (early-mid June).

I have compiled a list of components, and I'm looking for some opinions. Here's what I'm looking at (minus the keyboard and mouse; current build total = $2528.81):

MOBO ($399.99): SUPERMICRO MBD-X8DAi-O Dual LGA 1366 Intel 5520 Extended ATX Dual Intel Xeon Processor 5500 sequence (Nehalem-EP processor) Server Motherboard

RAM (2 @ $105.99 = $211.98): Crucial 6GB (3 x 2GB) 240-Pin DDR3 SDRAM ECC Unbuffered DDR3 1333 (PC3 10600) Triple Channel Kit Server Memory Model CT3KIT25672BA1339

PROCESSORS (2 @ $384.99 = $769.98): Intel Xeon E5520 Nehalem 2.26GHz 4 x 256KB L2 Cache 8MB L3 Cache LGA 1366 80W Quad-Core Server Processor

HEATSINKS (2 @ $39.99 = $79.98): Dynatron G666 60mm Double Ball Bearing CPU Cooler

THERMAL PASTE FOR HEATSINK ($8.99): Arctic Silver 5 Thermal Compound

HEATSINK BRACKETS [??] (2 @ 2.99 = $5.98): Dynatron DY-PBK-1366 Mounting Kit option avaliable for Intel Core i7 desktop motherboard

VIDEO CARD ($184.99): PNY VCQFX580-PCIE-PB Quadro FX580 512MB 128-bit GDDR3 PCI Express 2.0 x16 Workstation Video Card

HDD (2 @ $99.99 = $199.98): Seagate Barracuda 7200.12 ST31000528AS 1TB 7200 RPM 32MB Cache SATA 3.0Gb/s 3.5" Hard Drive

CASE (179.99): COOLER MASTER COSMOS 1000 RC-1000-KSN1-GP Black/ Silver Steel ATX Full Tower Computer Case

POWER SUPPLY ($134.99): COOLER MASTER UCP RS700-AAAAA3 700W ATX12V / EPS12V SLI Certified CrossFire Ready 80 PLUS SILVER Certified Power Supply

OPTICAL DRIVES (2 @ $25.99 = $51.98): Sony Optiarc Black 24X DVD+R 8X DVD+RW 12X DVD+R DL 24X DVD-R 6X DVD-RW 12X DVD-RAM 16X DVD-ROM 48X CD-R 32X CD-RW 48X CD-ROM 2MB Cache SATA DVD/CD Rewritable Drive

DISPLAYS (2 @ $149.99 = $299.98): ASUS VW224U Black 22" 2ms(GTG) Widescreen LCD Monitor w/ HDCP Support 300 cd/m2 1000:1 (ASCR 5000:1)

**QUESTIONS (please respond to any or all)**

1. What are your general impressions of this system? Am I missing anything obvious (connecting cables, perhaps)?

2. Do I need the heatsink brackets? The heatsink says that it does not come with a backplate, but I do not know what that means. Some customer comments indicated that the mounting kit was needed, but the mounting kit indicates that it is for Core i7 motherboards, which is not what I'm going to be using.

3. Do I need the thermal compound for the processor/heatsink?

4. Will these heatsinks fit in the case that I selected?

5. Is this video card capable of powering two displays for an extended desktop? The graphics card has two Displayport outs and one DVI out. I'm assuming that one display can be connected via DVI and the second display can be connected to a Displayport via Displayport-to-DVI adapter. Am I correct?

6. I selected ECC RAM. What is the difference between this and "registered" RAM? The "registered" RAM appears to be about twice the price of what I selected, but I do not know why.

7. Is the power supply I selected sufficient to power this system? Will it connect to all of these components?

8. I would love to go higher than 2.26 GHz, but the price increases are prohibitive. Are there ways of effectively overclocking these CPUs? Does overclocking impact computational accuracy or system reliability? Or will overclocking not be necessary because I will have so many cores and so much RAM? (Currently, my most powerful machine is a notebook running a 2.93 GHz Core 2 Duo w/ 4 GB DDR3 RAM.)

Thank you, in advance, for your help. My department will be purchasing the to-be-proposed components on my behalf, so it is critical that I (a) get the most for my money, since this opportunity will only come once and (b) purchase all the correct components on the first try.
May 10, 2009 4:47:18 AM

That is a workstation video card but im sure you could get a gtx 260 for that price and it has more memory, faster memory and 216 cores instead of 32.

All the gtx 260 doesnt have is the cuda drivers. But with the increased performance im not so sure they are important
May 10, 2009 6:10:31 AM

Actually, the GTX 260 does have CUDA drivers. What it doesn't have is 3D program specific drivers.

Tabakj, have you checked on whether or not there is CUDA support for Matlab and/or EEG calcs? I ask because I remember reading about a company using Nvidia cards for near-realtime CT scans. If people have started porting these medical programs into CUDA language, I would venture that support is probable. I know you can go to Nvidia's CUDA page and it lists all the different programs which use CUDA.

Using CUDA, you could skip the Dual-CPU setup and spend less on a few Nvidia cards. Heck, one GTX 280 can blow away a dual-quad setup in pure power.

Also look into ATI's stream processors to see what applications they support.

GPU acceleration is the very near future.

To answer your questions:

1) Not bad so far
2) The brackets are most likely to fit the heatsink to the LGA1366 socket which these Nehalem's are and so is i7. Heatsink manufacturers can't remake their heatsinks so they sell a bracket to adapt to the new socket(LGA775 is the prior socket)
3) I would use the Artic thermal compound - its far better than anything that will come with the heatsinks
4) I would use the Dynatron T667 for $30 each or the Intel BXSTS100A for $23 each. Both support 80w CPUs and the more expensive heatsinks support the 130w CPUs. The Arctic thermal paste will help drop the temps 2-3 degrees C.
5)Yes, the video card uses a DisplayPort to DVI adapter. With your current setup, you can easily get by with a $90 desktop video card or even the ATI FirePro V3750 for $150 or V3700 for $100 if you really want a Workstation card.

6) For the exact details of "Registered" ram, google it. For your needs, you don't need it. Also, with all Ram slots full, the motherboard maxes out at 1066 so using 1333 is not needed.

Do you know how much Ram Matlab and your other apps need? I ask because for another $200-250, you can get a board with more Ram slots and more Ram to fill them.

7) I would get a PC Power & Cooling as they tend to be the best quality.
Here is their 750w on sale for only $110 plus a $20 Rebate.
http://www.newegg.com/Product/Product.aspx?Item=N82E168...

And for 2 CPUs, you need a Molex to 8 pin CPU power plug which only cost $5.

8) Sorry, but there are ZERO ways of overclocking the Xeon CPUs. Intel knew if there was a way that they would lose millions of dollars. However, these Nehalems have their own "Turbo" mode beginning with the 5520. Also, the chips below the 5520 don't have Hyper-Threading. The Turbo mode increases the speed slightly on all four cores during heavy use for short periods of time(for the 5520, it goes to 2.33 from 2.26).

Have you considered the performance difference of 2 - 2.26GHz Nehalems to a single i7 920 overclocked to 3.4GHz? For Matlab, it probably won't induce/benefit from Hyper-Threading from the 2.26GHz chips but definitely from the i7 at 3.4GHz. This means there would be 8 "cores" running at 1.7GHz or even 1.8GHz if you OC to 3.6GHz. There is not much of a performance difference between 8 2.26GHz cores and 8 1.8GHz cores but there is a huge price difference.

I know that I'm looking at the Hyper-Threading "cores" vs actual cores in a very simplistic way but the performance difference doesn't justify the additional $500.
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May 11, 2009 3:39:04 PM

Thanks for your replies! Very helpful.

Matlab does have (very) limited CUDA support so far (Nvidia plugin). Most of the EEG computations are performed by a custom Matlab toolbox (EEGLAB), and I have no idea when EEGLAB might support GPU acceleration.

So, for now, I think it probably makes sense to go with the dual quad-core set up. But, I definitely want to make sure that I have the option of expanding my system with more powerful GPUs down the road.

--In terms of a "workstaton" vs. "desktop" GPU, what is the difference? Are these the same graphics cards, just repackaged?
May 12, 2009 4:57:24 AM

Workstation vs Desktop GPU: the main difference is in the drivers. Desktop drivers are geared to get max performance in games whereas Workstation drivers are geared for max performance in 3D apps. Also, Workstation cards tend to have longer warranties and much better tech support. For example, Nvidia will customize/tweak their driver for Maya if a customer needs it.

Back to performance: I don't know if you must spend $2500 but the performance difference between a dual 2.26GHz vs a single i7 overclocked to 3.6GHz isn't that much. If the computations take 20hrs with the dual setup, the i7 setup shouldn't take more than 24-26hrs.

For future upgrades: upgrading the i7 will be much cheaper especially when Intel releases their 8 core CPUs at the end of this year/beginning of next year. I can't predict what the prices will be for their Xeon 8 core but I would bet they start out over $600 each compared to $400-500 for a much a higher clocked i7 8core.

Furthermore, when CUDA support for Matlab is readily available, it won't matter what CPUs you have because a single GPU is extremely powerful.

I'm just trying to put everything in perspective and save you some money.

For future upgrade, that Supermicro board only had 2 PCI Express x16 slots so that will limit you for GPU acceleration.

A very good reason to go with the dual xeon setup is amount of Ram. I don't know what Matlab and the specific computations need for Ram and whether 12GB vs 24GB makes any real difference.

Have you checked this page for Matlab plug-ins? There are a couple if you search "Matlab".
http://www.nvidia.com/object/cuda_home.html#state=home
May 12, 2009 5:38:55 PM

Thank you. Again, this is very helpful.

I'm thinking that it might make more sense to build a (single-processor) Core i7 920 system. If I do this, I don't think I'll save much by building my own system (vs. purchasing a CTO HP Pavillion Elite m9600t series).

So, now the question is whether it would make sense to build my own i7 vs. purchasing a CTO HP machine. I am pretty confident that I would have better quality components in a machine that I would build, but there is a certain amount of security that comes along with a 3-year HP warranty. What are your thoughts on this? I am not very familiar with overclocking -- would I be able to OC with whatever mobo would come in a CTO HP machine, or do I need specific mobos to OC my CPU?
May 12, 2009 9:53:12 PM

Hi,

I'm building a similar system and I have difficulties to get some information... Can you tell me how you handle the fact that the board as two 8-pin EPS12V and the power supply only one.
Have you used a splitter to split the 8-pin, a molex to 8-pin converter or a different solution ?

thank you
May 13, 2009 4:21:39 AM

daclo, you can buy a Molex to 8 pin adapter for about $5.

About the HP: I would put money on their PCs not allowing overclocking. I would also bet that you can save money building it yourself.

I remember Dell offering Overclocking once, but I think it was just pre-Overclocked and not able to be changed.

For Overclocking yourself, pretty much any i7 board you buy will allow for easy overclocking to 3.4-3.6GHz. Some of the more expensive boards are designed for those who want 4.0GHz.

For warranty, PC Power & Cooling come with a 5yr, Intel CPU a 3yr, ASUS boards come with a 3yr (I think), Ram is lifetime, Hard Drive is 3 or 5 yrs.
May 14, 2009 7:07:51 PM

I contacted Intel and they said the multipliers on the Xeons (5500) are unlocked. I've read that people have dropped them into Core-i7 motherboards and overclocked them just fine. What we seem to be missing is a dual Xeon Nehalem-EP motherboard with BIOS that will let us do it.
May 14, 2009 7:53:34 PM

^ I was pretty sure you can't use 5500 series cpu's in core i7 motherboards, I know that you can use w3500 series cpu's in them though.

and wouldn't OC'ing two 130w cpu's to high levels put you in the 200w each CPU area? that's 400w just for CPU's, add in a 200w gfx card, the HDD's, ram, fans etc and it will be using loads of energy.
May 14, 2009 8:40:00 PM

i don't know about the wattage but i am not concerned about the power. the difference between two CPUs running at 2.00GHz and 4.00GHz to compute/render video for example, in time saved, is well worth the added cost per kWh. After all, 1,000 Watts only costs about 11¢ per hour. So, if I'm going from 800W to 1000W, the extra 2¢ per hour isn't really much to consider.

regarding the 3500 vs 5500, if you have a look here, you can see (and other sites) that people are successfully using the Xeon 5580 in Core i7 boards... http://www.bit-tech.net/hardware/cpus/2009/03/30/intel-...

personally, i don't know what Intel is doing letting us buy the cheap models and overclock them. doesn't seem like a great business model, but it makes me happy!

i'm just waiting on a dual board with good overclocking BIOS!!

May 15, 2009 6:22:34 AM

To be honest, spending $1000 for a Xeon is really stupid when you can spend less than $300 on an i7 an get the exact same result.

Secondly, Video rendering & encoding is done OVERNIGHT so increasing performance 10-20% is worthless because you would never notice it. (This is very general and I know some have larger projects with many effects and layers but those that require minimal rendering time usually can afford small rendering farms - you can figure with a single quad core to get 1 minute of video rendered in about 8 minutes so even an hour long video would only take 8hrs)

Also, you will NEVER find a dual-Xeon board with Overclocking enabled. Who do you think makes the chipsets that work with the Xeons? INTEL. Do you think they would throw Millions out the door and allow overclocking? Not in a million years.

Last point, those "Unlocked Multipliers" referenced is the same as a 920 or 940 i7 where you can drop the multiplier but NOT increase it.
May 20, 2009 1:10:46 AM

tabakj,

IMO you are at the borderline between Workstation and server. Something very important to consider, where will this machine live? It is going to generate some serious heat and require some serious cooling. If you have access to a proper data center I would recommend that you consider the Dell R610 and R710 servers. I just ordered 4 R610's with Dual E5220's, 12GB DDR3 1333 (6x2GB), rails, OS, dual power supplies, etc. and came in around $3100 each. A quick config of a R710 with those CPU's and memory lists for $2657 which can easily get below your $2500 when you call their sales reps. FYI - If you want that memory config in the R610 you have to work with a sales rep as that the website does not offer it.

Another consideration: Yes you get hardware warranties from the hardware vendors (Intel, Cosair, etc.) but how many of them give you next day service? Waiting 7-14 days+ for a standard RMA from the hardware vendor is quite a long time when this is a business need and not a hobby PC.

Don't get me wrong. I have built more PC's than I care to count. There are definite advantages to building your own machine. That being said there are also definite advantages to using a system vendor. The trick is to carefully define your requirements.

-rh

P.S. Please let us know what path you end up taking.
June 18, 2009 6:08:25 PM

specialk90 said:
To be honest, spending $1000 for a Xeon is really stupid when you can spend less than $300 on an i7 an get the exact same result.

Secondly, Video rendering & encoding is done OVERNIGHT so increasing performance 10-20% is worthless because you would never notice it. (This is very general and I know some have larger projects with many effects and layers but those that require minimal rendering time usually can afford small rendering farms - you can figure with a single quad core to get 1 minute of video rendered in about 8 minutes so even an hour long video would only take 8hrs)

Also, you will NEVER find a dual-Xeon board with Overclocking enabled. Who do you think makes the chipsets that work with the Xeons? INTEL. Do you think they would throw Millions out the door and allow overclocking? Not in a million years.

Last point, those "Unlocked Multipliers" referenced is the same as a 920 or 940 i7 where you can drop the multiplier but NOT increase it.



I'm talking about buying XEON E5520s for $375 each. These are upward, not just downward, multiplier unlocked. If you put one in an i7 board, you can overclock. It is the BIOS which is holding us back. This is all my understanding because I've read multiple accounts of people putting the 2.x GHz XEONs into i7 boards and overclocking them. So in a UP config, they are overclocking just fine. We just need a motherboard with the extra slot and QP so we can drop two CPUs in. As for rendering, every bit helps. 4.0GHz works 2x faster than 2.0GHz. With 16 threads, CUDA, etc, we're getting pretty close to live rendering depending on resolution and complexity, as I see it. But I do agree with your well-put point that typically, you render overnight. Sometimes though, you want to work, render, work, render, work, render... etc. in order to see the final quality as you create. 4.0 GHz is nice with one i7, but with two Xeons, it's 1.5x faster. 50% faster in this kind of workflow means a lot (to me anyhow.)
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