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Help needed! Build Dual Xeon Quad for Molecular Simulation

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October 23, 2008 7:00:05 AM

Hi, all

I am planning to build a dual Xeon Quad Core for my research in molecular simulation. i.e. I want to have 8 cores totally. For the job I am doing, I will some parallel calculations (using 4 cores at the same time with communications among the cores), but most of the time, I may be just running several jobs (like 7 or 8 different cases) on different cores, each taking 10 hrs to 100 hrs to run). Other information:

1. I am a student with limited office space, so buying 2 computers, each with a Quad Core is not good for me. I don't want to have two computers either since then I need to compile my code on two computers.
2. CD-ROM, Monitor, Keyboard, Mouse is not necessary. The department has some old ones I can use.
3. Some visualization is necessary but the quality not very essential (Only used when I visualize my computation results for presentation).
4. The I/O during the computation is moderate, about 50 to 100 MB per hour for each job / case.
5. I am buying this with my own money, not a funding ... so I have a very limited budget. You know ... graduate student is not a real job and the paycheck is tiny.

Before posting this message, I have read this thread in detail:

http://www.tomshardware.com/forum/251101-28-build-dual-...

Particularly, the reply by Turas was VERY VERY helpful. According to what is stated there I have researched extensively (with google...) and here is my setup. Please give me some suggestions. It will be greatly appreciated!!
I am building the system according to Dell Precision T7400

http://www.dell.com/content/products/productdetails.asp...

1. Motherboard
Asus DSAN-DX Server Motherboard - Dual Socket 771, Intel 5100, Asus PIKE Ready, 1333/1066/800MHz FSB, Reg ECC RAM, PCIe x16, SATA II RAID, VGA
$335 (tigerdirect)

2. CPU (Two *Xeon E5420)
Intel Xeon E5420 Processor BX80574E5420A - 2.50GHz, 12MB Cache, 1333MHz FSB, Harpertown, Quad-Core, Retail, Socket 771, Processor with Active Heatsink
$330 * 2 (Buy.com)
(Replacing with E5410 could save $30 each, but I am reluctant because CPU is the most important part for my purpose)

3. Two of the following (totally 8G)
Kingston 4GB (2 x 2GB) 240-Pin DDR2 FB-DIMM ECC Fully Buffered DDR2 667 (PC2 5300) Dual Channel Kit Server Memory - Retail
$125 * 2 (buy.com?)
The computation is somewhat memory intensive. Ideally I would like to have 16G, but really can't afford that now.

4. Hard Drive
Seagate Barracuda 7200.11 1.5TB Hard Drive ST31500341AS - Serial ATA 7200/32MB/SATA-3G
$190 (Tigerdirect)
BTW, I have a spare 80G SCSI hard drive.

5. Video card
PNY GeForce 8400 GS 256MB DDR2, PCI Express, Supports 512MB, (Dual Link) DVI, VGA, HDTV
$50 (Tigerdirect)

6. Case
ThermalTake Armor VA8000BWS Black Full Tower Case
$150 (Tigerdirect)

7. PSU
Ultra Products ULT40064 X3 1000-Watt Energy Efficient Modular Power Supply
$220 (JR.com)

8. OS
CentOS Linux 5.2 Enterprise 64bit
Free.

-------------------------------
Total:
Approx. $2000

The list price above are all the lowest I can find online. But still is a little bit beyond my budget, although if there is no way reducing it I would accept this cost.

Questions:
1. Does the setup suitable or my purpose? Do the capabilities of the components match overall? Are there any obvious bottle-necks or incompatabilities?

2. Is any of them unnecessarily high compared to others so that I can downgraded it to save some money?

3. If I am willing to wait until the end of November, would the system-build price drop by a noticeable amount ... ? Like save $200? For example, a new hardware enter the market and the current ones drop price, or by taking advantage of the Thankgiving deals.

4. Ideally, I wan to have the Linux system installed on the 80G SCSI hard driver and my own files on the 1.5T SATA driver. Is that possible or easy to do? If yes, any pointers or hints?

I am really new to hardward and system building. Your comments and suggestion are greatly appreciated! Thanks very much.

Best,
Henry
Email: nomadzju _AT_ gmail dot com

Quote from Turas:
Quote:

-----------------------------------------------
I have a Dual XEON Setup using an ASUS MB. I love the MB. It is a different model but love the quality. First off your case will not fit that motherbord. The XEON boards are either SSI CEB or EATX (Extended ATX). So you will need to fork out more for a case. I am using the Thermaltake Armor which fits them nicely. I belive the Antec P190 also fits EATX but I hate that it comes with it's own power supply.

The RAM is also not correct, you need FB-DIMMs. Also I think the machine is probably an overkill if you are only loading it with 2GB of ram. FB-DIMM's get hot and I mean real hot. You need to get something to cool them or have good airflow over them at least. Mine with very little airflow are hat 84 and 77 celcius. Here is a link to some FB-DIMMs
http://www.newegg.com/Product/Prod [...] 6820134649

I am using the 5355's so I believe my CPU's would be hotter then yours. With the 5355 passive cooling is not enough. I used the dynatron's active coolde with the fan on the side and it cooled the CPU nicely. It also cooled the memory more and everything was running great. The price to pay was they were loud as hell. I eventually took them out and put on a water loop.

I definately recomend some case fans although the number and speed may vary depending on how you decide to cool the CPU and memory.

I don't see a PSU listed. but these boards require 2- separate 12 v/4pin connectors. My PSU didnot have them but I got a cable that makes them from the standard non sata power connector.

Message edited by Turas on 06-15-2008 at 04:30:16 AM

---------------
Turas
--------------------
ASUS DSEB-DG MB, Thermaltake Armor Chasis, Dual XEON 5355 2.66Ghz, 8GB Ram, ATI 3870,
Dell 2707WFP Monitor, Adaptec 31605 SAS RAID, 4 -10K 2.5 SAS Seagate drives, ARECA 1680ix w/4GB Cache, 4 WD 300GB VR HD Drives,Reserator X
-----------------------------------------------
October 23, 2008 8:01:17 AM

I would STRONGLY recommend not going with Xeons for molecular simulation, since this comes under the category of high performance computing, which is very sensitive to memory bandwidth and latency. I recently tested some of my own high performance codes on the intel chips, and they just fall over at more than two jobs per core (ie no speedup at all). As a result we have bought a quad core opteron system, which gives much better performance running 8 codes (or one parallel job over 8 cores).

If you can wait then I would also recommend the Nehalem Xeons which are supposedly to be released imminently - these are likely to be faster than the opteron chips, but at what price I am not sure. Also, the opterons dont need expensive FBDIMMS, which should lower the cost quite a bit. One final point - have you tried Ubuntu? I have found it a lot easier to configure and use than Redhat/CENTOS, it maybe worth a try...
Anonymous
October 23, 2008 9:10:27 AM

If you are trying to save money, I don't think you need the 1000W power supply, or that expensive case. You should also look at CUDA, which has been used for MD simulations
Related resources
October 23, 2008 9:37:43 AM

The PSU is a good choice as your system with 2 multi core cpu and a decent video card will require a substantial amount of power.The 8400 is just not good enough for what you want to do.I recommend a 8800GTS 512 or a similar ATI card.A server board is a good way to get what you want all in one comp.However,NVIDIA GPU's are great for doing calculations,but only the higher end ones.The 1000 watt PSU will be good for future proofing and you'll only be required to upgrade a couple of pieces of hardware 2 yrs down the road.Just to let you know,the higher end NVIDIA cards do cuda quite well.Goodluck.OH and I would go with the AMD opterons as they are designed more for doing what you want than the xeon.And cheaper too.

Dahak

M2N32-SLI DELUXE WE
X2 5600+ STOCK (2.8GHZ)
2X1GIG DDR2 800 IN DC MODE
TOUGHPOWER 850WATT PSU
EVGA GTX 260
SMILIDON RAIDMAX GAMING CASE
ACER 22IN WS LCD 1680X1050
250GIG HD/500GIG HD
G5 GAMING MOUSE
LOGITECH Z-5500 5.1 SURROUND SYSTEM
500WATS CONTINUOUS,1000 PEAK
WIN XP MCE SP2
October 23, 2008 2:59:02 PM

Thanks very much for the reply! Here is some follow-up.

Quote:

I would STRONGLY recommend not going with Xeons for molecular simulation, since this comes under the category of high performance computing, which is very sensitive to memory bandwidth and latency. I recently tested some of my own high performance codes on the intel chips, and they just fall over at more than two jobs per core (ie no speedup at all). As a result we have bought a quad core opteron system, which gives much better performance running 8 codes (or one parallel job over 8 cores).

What model of opteron do you think would be comparible to Xeon 2.5GHz (in terms of single job)? I checked them briefly and it seems that they generally have lower frequency (1.8 to 2.0 GHz). In addition, the L2 cash is smaller 4*512K. Why do they have better preformance? Is it because they have L3 cash as well, or is it because the L2 cash is not a good indicator? If you only run 1 job per core (and 8 jobs at the same time on 8 cores) , would 2*operton still be better than 2*Xeon?

Also, if I change 2*Xeon above to 2*Operton, would the mother board etc. and other components need to be changed? (Other than that FBDIMM can be replaced by DIMM).

Quote:
they just fall over at more than two jobs per core (ie no speedup at all). As a result we have bought a quad core opteron system, which gives much better performance running 8 codes (or one parallel job over 8 cores).

Can you detail on that? For, the comment "no speedup", which two cases are you comparing? How many nodes and cores are you running for the 8 jobs? Are then on the same motherboard or connected by network? Do they communicate?
Since this is the part I am concerned with the most, more details would really be helpful.
Quote:

If you can wait then I would also recommend the Nehalem Xeons which are supposedly to be released imminently - these are likely to be faster than the opteron chips, but at what price I am not sure. Also, the opterons dont need expensive FBDIMMS, which should lower the cost quite a bit.

I guess the newly released model would generally be over-priced...
My intention was to wait for the new release model to drive the existing models on the market to lower price.
October 23, 2008 3:52:51 PM

About the comparison of Xeon/Opteron:

I also noticed that the motherboard would need to be changed as well if Opteron are used. I only saw a few TYAN mother boards which supports opeteron's Socket F.

In addition, in the same price range, (around $300), Opteron 2.1GHz is about the same as price as Xeon E5420 (2.5GHz). However, Opteron 2.3Ghz and 2.5Ghz are MUCH more expensive. Why is that?
October 23, 2008 4:36:07 PM

nomadzju said:
About the comparison of Xeon/Opteron:

I also noticed that the motherboard would need to be changed as well if Opteron are used. I only saw a few TYAN mother boards which supports opeteron's Socket F.


Yes, the mobo would need to be changed as Xeons are Socket 771 and Opterons are Socket1207 (2xxx series) or Socket940 (1xxx series). The mobo makers you want to be looking at for either dual socket Xeon or Opteron are Tyan and Supermicro. Personally I recommend a Supermicro mobo running the MCP55 chipset, something like the H8DMi-2 would be good as it has onboard VGA and supports dual/quad core Opterons.

nomadzju said:
In addition, in the same price range, (around $300), Opteron 2.1GHz is about the same as price as Xeon E5420 (2.5GHz). However, Opteron 2.3Ghz and 2.5Ghz are MUCH more expensive. Why is that?


Short answer and without threatening the start of a long discussion or flame war, Opterons have an Integrated Memory Controller and different uArch which translate into less GHz but equal or better performance to Xeons of the same or higher speeds. Opterons have bested Xeons in 2-way and 4-way settings as well as scaling due to the IMC and "more efficient" uArch.

As an alternative, look into a 1000 series quad core Opteron and a mobo like the Supermicro H8SMi-2 which has integrated VGA, NIC, and 6-SATA2 ports. You'd still get the advantages of quad core Opteron with the IMC and cheaper ECC DDR2 800 memory. Perhaps something like the Supermicro H8SMi-2 ($250) and Opteron 1354 ($270) and a 2GB kit of Crucial ECC DDR2 800 memory ($120). That would make for a solid workstation for about $650! Not bad at all, I say...

As another alternative, wait until Spring 2009 and check out an X58 mobo with a Corei7. Preliminary reports show the Corei7 to be great at multi-tasking as well as re-introducing HyperThreading for a total of 8 logical cores. Nice!

Good luck!

PS - all prices from Newegg...

October 23, 2008 8:34:01 PM

Thanks for the very nice suggestion! I am still debating getting a 4-core system for about $700, or a 8 core-system for about $2000. What if I go for 8 core, and get two Opteron 2350 (each about $260). Also I can save some money since FB DIMM is not needed. Do you have any suggestion for the 8 core choice with Opteron? What MOBO would you recommend for the dual opteron? Would other components listed above still suitable (except memory)?

I did read some report showing the scalability of Xeon when two 4-core CPUs are used, the processor-memory communication is a bottleneck.

Quote:
As an alternative, look into a 1000 series quad core Opteron and a mobo like the Supermicro H8SMi-2 which has integrated VGA, NIC, and 6-SATA2 ports. You'd still get the advantages of quad core Opteron with the IMC and cheaper ECC DDR2 800 memory. Perhaps something like the Supermicro H8SMi-2 ($250) and Opteron 1354 ($270) and a 2GB kit of Crucial ECC DDR2 800 memory ($120). That would make for a solid workstation for about $650! Not bad at all, I say...
October 24, 2008 2:45:01 AM

Any follow-up from the experts?
October 24, 2008 1:30:36 PM

nomadzju said:
Thanks for the very nice suggestion! I am still debating getting a 4-core system for about $700, or a 8 core-system for about $2000. What if I go for 8 core, and get two Opteron 2350 (each about $260). Also I can save some money since FB DIMM is not needed. Do you have any suggestion for the 8 core choice with Opteron? What MOBO would you recommend for the dual opteron? Would other components listed above still suitable (except memory)?


Correct, an Opteron based workstation would use ECC DDR2 memory and not FB-DIMMs which is a big costs savings.

For an 8-core Opteron machine, you want a dual Skt1207 mobo and two quad core Opterons. I highly recommend Supermicro mobos using an nVidia chipset, something like the Supermicro H8DMi-2 would work very well as it has integrated VGA, NIC, and lotsa SATA ports. Two Opteron 2350's ($260each), 8GB DDR2-667 Kingston RAM (4 x 2GB @ $260), plus the Supermicro H8DMi-2 ($360) mobo would make for a very nice machine!

As far as the other components (case, hard drive, psu, ROM's, etc), choose whatever works best for you. Given that the Supermicro H8DMi-2 has onboard VGA, a video card is not necessary unless you want to run any 3D applications.

All things considered, using the above mentioned mobo and cpu's, plus the other components you've listed, you could build this rig for under $2000.
December 1, 2008 12:12:39 AM

Follow the suggestions from the experts in this forum, the following configuration is planned. The replies above are greatly appreciated!!!

Any suggestions? Am I missing something?

Planned configuration:
---------------------------------------
1. Mobo:
SUPERMICRO H8DME-2-O Dual 1207(F) NVIDIA nForce Professional 3600 Extended ATX Server Motherboard - Retail ($370)
http://www.newegg.com/Product/Product.aspx?Item=N82E168...
Supermicro H8DME-2 is chosen over H8DMi-2 for better OS compatibilities.
(What are the essential differences between H8DME-2, H8DMi-2, and H8DAE-2?)
Mobo / system compatibility: http://www.supermicro.com/Aplus/support/resources/OS/OS...

2. CPU:
AMD Opteron 2376 Shanghai 2.3GHz 45nm Socket F 75W Quad-Core Server Processor - Retail ($380*2)
2378 Model 2.4GHz would cost ($520*2), i.e. $280 more
http://www.newegg.com/Product/Product.aspx?Item=N82E168...

3. HeatSink: (Is it required if Retail CPU purchased?)
Supermicro Active Heatsink for AMD (Socket F) CPU - SNK-P0024AP4 ($60)
http://www.buy.com/prod/supermicro-active-heatsink-for-...

4. Is thermal compound needed?

5. Memory: (4*2G, $150)
Kingston Standard 256M X 72 Parity 800MHz 240-pin Registered DIMM (SDRAM-DDR2, 1.8V, CL6, FBGA, Gold)
http://www.ec.kingston.com/ecom/configurator_new/PartsI...
Or buy on amazon:
http://www.amazon.com/Kingston-ValueRAM-240-pin-PC2-640...

6. Case + PSU:
Cool Master Computer Case: ($430)
COOLER MASTER COSMOS 1000 RC-1000-KSA2-GP Black/ Silver Steel ATX Full Tower Computer Case 1000W Power Supply - Retail
http://www.newegg.com/Product/Product.aspx?Item=N82E168...

7. Hard Drive:
1TB. Any brand. $120

Optional:
---------------
8. Video Card (NOT required. Mobo has onboard video card).
ATI Fire pro V3700 ($84)
http://www.newegg.com/Product/Product.aspx?Item=N82E168...

9. Audio Card: ($15)
StarTech PCISOUND4LP 4 Channels 16-bit 48KHz PCI Interface Low Profile Sound Card - Retail
http://www.newegg.com/Product/Product.aspx?Item=N82E168...

Do not need keyboard, mouse, DVD-ROM.

-----------------------------
Total price: $2000 to $2200
December 1, 2008 12:21:27 AM

An alternative plan using i7 (without many details):
CPU $570 (i7 940)
Mobo $319
Video Card $70
http://www.newegg.com/Product/Product.aspx?Item=N82E168...
PSU $180 (850W)
Case $200
Memory $269 (3*2G DDR3)
Hard drive $140 Seagate 1.5T
------------------------
Total $1748

Which comes out not far from the Dual opteron options. Opteron has real 8 cores so I think 8-core opteron is slightly better.



December 1, 2008 3:52:18 PM

any critique?
December 1, 2008 4:51:59 PM

if you plan to run mostly singlethreaded apps on different cores, why not go for a single cpu, quad core like a q9xxx? You are looking at reducing the length of the simulations so you could achieve that result by overclocking slightly your processor and call it a day for somewhat less money.

I'm just saying, there are several choices out there :) 
December 2, 2008 1:25:32 PM

Because I may want to do a small-scale parallel computing (with MPI), using 4 or 8 processers. The molecular simulation is easily parallized, and would reduce the time by a factor of about 3 or 6 (slighly worse than linear), which is a huge saving.

I am wondering whether I am missing any parts or there are any unnecessary or incompatible parts (like heat sink).

Any comments would be appreciated!

Heng
December 2, 2008 2:27:29 PM

afaik, a q9xxx still has 4 cores that can run up to 4-4.5ghz on air cooling, each. That's a lot of power for very cheap. I wouldn't discard that option just yet.

Regardless, if your dept is serious about those types of calculations, you should perhaps talk to your Chair and make a proposal to buy a beefier option (such as a nice Sun Blade t6xxx or whatever suits your needs). I remember hearing mine discussing his research setup in a class a year ago. Apparently, they (Sun micro) have nice rebates at the moment.
This would make a whole lot more sense than buying your own computer and walking out with it when you are done. If the dept. had one, you'd save a lot of money and the setup would be repaying itself by being used by all the other grads who are possibly also trying to find some computing time. In any case, I doubt TH is really the resource to discuss that part ;) 
!