Solid Workstation Setup

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pkkevin

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Oct 18, 2007
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1) What will you be doing with this PC? Gaming? Photoshop? Web browsing? etc

A workstation for Bioinformatics Lab
I will be using this computer for programing, running some genome analysis, assembly, that are are CPU intensive and RAM demanding.
However, I don't need top of the line server stuff, real demanding computation will be done on our computer cluster.
There will be no upgrading of this once it is built.

2) What's your budget? Are tax and shipping included?

Less than $1,200, shipping included. (no tax from newegg.com) Can be more if justifiable.

3) Which country do you live in? If the U.S, please tell us the state and city if possible.

Saint Louis, MO

4) What exact parts do you need for that budget? CPU, RAM, case, etc. The word "Everything" is not a valid answer. Please list out all the parts you'll need.

CPU, MB, RAM, case, PSU, SSD, HD, DVD drive, mouse and keyboard

5) If reusing any parts, what parts will you be reusing? Please be especially specific about the power supply. List make and model.

I will reuse my current monitor.

6) Will you be overclocking?

No, I need stability over speed

7) What is the max resolution of your monitor? What size is it?

22" 1920x1080 I would like to use dual screen if possible, Not included in the budget.

8) When do you plan on building/buying the PC?

In the next few weeks.

9) What features do you need in a motherboard? RAID? Firewire? Crossfire or SLI support? USB 3.0? SATA 6Gb/s? eSATA? Onboard video (as a backup or main GPU)? UEFI? etc.

Just the standard, no specific need.

10) Do you already have a legit and reusable/transferable OS key/license? If yes, what OS? Is it 32bit or 64bit?

Yes, I am planing to use Ubuntu linux.


I was thinking about just getting an off-the-shelf workstation from dell, but since I am sort of in the know of hardware stuff ( built my last two PC ) and it is ridiculously expansive for what I want to get(~$2000~$4000), I am now considering the possibility to build my own workstation.

Initially I was just trying to get the PC setup with i7-2600k with Z68 and 32Gb of RAM. However, I realized the non-ecc nature of this build and I have been looking in the "server grade" hardware.

I read this thread: http://hardforum.com/showthread.php?t=1593192
But did not really find any conclusion to my situation and would like to ask for help and opinions.

Here is my preliminary build:

CPU: Intel Xeon X3440 Lynnfield 2.53GHz LGA 1156 95W Quad-Core Server Processor http://www.newegg.com/Product/Product.aspx?Item=N82E16819117225
MB: SUPERMICRO MBD-X8SIL-F-O Xeon X3400 / L3400 / Core i3 series Dual LAN Micro ATX Server Board w/ Remote Management http://www.newegg.com/Product/Product.aspx?Item=N82E16813182211
RAM: Kingston 32GB (4 x 8GB) 240-Pin DDR3 SDRAM DDR3 1600 ECC Registered Server Memory DR x4 w/TS Model KVR1600D3D4R11SK4/32G http://www.newegg.com/Product/Product.aspx?Item=N82E16820239015
case: Antec Three Hundred Black Steel ATX Mid Tower Computer Case http://www.newegg.com/Product/Product.aspx?Item=N82E16811129042
PSU: CORSAIR Builder Series CX600 V2 600W ATX12V v2.3 80 PLUS Certified Active PFC Power Supply http://www.newegg.com/Product/Product.aspx?Item=N82E16817139028
SSD: Crucial M4 CT128M4SSD2CCA 2.5" 128GB SATA III MLC Internal Solid State Drive (SSD) with Transfer Kit http://www.newegg.com/Product/Product.aspx?Item=N82E16820148448
My OS will be on SSD and other common used files
HD: Western Digital Caviar Blue WD10EALX 1TB 7200 RPM SATA 6.0Gb/s 3.5" Internal Hard Drive -Bare Drive http://www.newegg.com/Product/Product.aspx?Item=N82E16822136767
I need HD to store less often used data

I have couple of questions:

0) Before all the other questions, I would like to first ask if this self-build workstation going to be less stable compared to Dell workstations?
I think it is really fun and money saving if all this work out, I am also confident that I sould be able to complete this. But on the other hand, I don’t want to spend a large amount of time just trying to figure what went wrong if things does not work smoothly.

1) Does the ECC really matter? If not, is i7-2600K/Z68/nonECC platform setup better bang for the buck?
2) I read that Registered memory takes performance hits, is it noticeable?
3) I think the RAM will work with MoBo and CPU, does it?
4) I will be doing a lot of disk IO, does the WD Black justify its extra price? On paper, it seems that Blue and Black don't have significant difference.
5) If I want dual monitor, is it possible on this MoBo? I am assuming I need dedicated GPU? (any cheap GPU that can do dual screen will do if needed)
6) Is the power supply overkill?
7) I am assuming that Ubuntu Linux should not have hardware compatibility problems with any above mentioned setup?

Thanks!
 
0) If you select the right parts, no it won't be less stable. However a lot of the parts you chose aren't that great. But we'll get to that in a bit.

1) For your kind of usage, yes ECC matters. If this was a home PC, I would have said no. However considering that is for scientific and heavy duty programming purposes, I'd highly recommend ECC RAM.

2) AFAIK, not really.

3) I don't know to be honest. The RAM speed alone suggest that it may not work as the Xeons don't officially support ram speeds above DDR3 1333. So I'd try to find Kingston DDR3 1333 8GB ECC Registered RAM instead.

4) Nope. In fact, I wouldn't recommend that WD drive at all if you want a fast drive. I recommend these drives instead:
$120 - Samsung Spinpoint F3 HD103SJ 1TB 7200 RPM SATA 3.0Gb/s Hard Drive
$120 - Hitachi Desktar 7K1000.D HDS721010DLE630 1TB SATA 6.0Gb/s Hard Drive

5) You would need a dedicated GPU if you want dual GPU.

6) No but it's not that great of a buy considering that this higher quality, modular, and similar amperage Seasonic PSU costs around that same price:
$66 - SeaSonic M12II 520 Bronze 520W Modular PSU

7) AFAIK, no.

I should note that the the CPU and mobo are actually out of date now. The Xeon X3440 is slower than the 2600K or Xeon E3-1230 (cheapest Xeon version of the SB CPUs with HT) by about 10 to 15% clock for clock. And that's not factoring the higher clock speeds too of those CPUs. Since its out of date, you might have trouble fiding the CPU and motherboard for a reasonable price. There are server LGA 1155 mobos out there but the main problem is the RAM: They only use ECC Unbuffered RAM but they only have 4 DIMMs. As such, you would either be stuck with 16GB of RAM max or paying a large amount of money for hard to find 8GB unbuffered ECC RAM.

Case wise, that case is relatively cramped and has little to no cable management. I recommend this case instead:
$50 - NZXT Source 210 Elite Black ATX Case
$50 - NZXT Source 210 Elite White with Black Front Trim ATX Case
 
Danny Bui said:
1) For your kind of usage, yes ECC matters. If this was a home PC, I would have said no. However considering that is for scientific and heavy duty programming purposes, I'd highly recommend ECC RAM.
Click to expand...
Got it, I think that make sense and it is also why I moved to Xeon platform with ECC.


Danny Bui said:
6) No but it's not that great of a buy considering that this higher quality, modular, and similar amperage Seasonic PSU costs around that same price:
$66 - SeaSonic M12II 520 Bronze 520W Modular PSU
Click to expand...

Thanks for the recommendation!

Danny Bui said:
I should note that the the CPU and mobo are actually out of date now. The Xeon X3440 is slower than the 2600K or Xeon E3-1230 (cheapest Xeon version of the SB CPUs with HT) by about 10 to 15% clock for clock. And that's not factoring the higher clock speeds too of those CPUs. Since its out of date, you might have trouble fiding the CPU and motherboard for a reasonable price. There are server LGA 1155 mobos out there but the main problem is the RAM: They only use ECC Unbuffered RAM but they only have 4 DIMMs. As such, you would either be stuck with 16GB of RAM max or paying a large amount of money for hard to find 8GB unbuffered ECC RAM.
Click to expand...

Very good point. I was debating about the E3 vs X3440 platform also. But went with the X3440 because of the larger RAM size within budget.

I guess 32GB is not really important for my workstation since I have large cluster to do RAM demanding calculations.

The other benefit I realize going with E3 will be the SATA III 6.0 Gb/s port, will this be a noticeble difference between SATA 3.0 Gb/s?

Going with
CPU: E3-1230 http://www.newegg.com/Product/Product.aspx?Item=N82E16819115083
MB: SUPERMICRO MBD-X9SCM-O LGA 1155 Intel C204 Micro ATX Intel Xeon E3 Server Motherboard http://www.newegg.com/Product/Product.aspx?Item=N82E16813182254
RAM: 2x Kingston 8GB (2 x 4GB) 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10600) ECC Unbuffered Server Memory Model KVR1333D3E9SK2/8G http://www.newegg.com/Product/Product.aspx?Item=N82E16820139262

and the other recommended stuff leaves me at around $900

Will this combo work well?

If I were to increase SSD to 256gb or HD to 2TB, any solid recommendations?


Danny Bui said:
Case wise, that case is relatively cramped and has little to no cable management. I recommend this case instead:
$50 - NZXT Source 210 Elite Black ATX Case
$50 - NZXT Source 210 Elite White with Black Front Trim ATX Case
Click to expand...

Thanks a lot for the recommendation! it looks like to fit my need much better than the Antec case.


I really appreciate your help!! Thanks so much for helping me sort this out.
 
PersonalJ said:
The newer intel Xeon E5 series supports registered ECC memory. http://www.intel.com/content/www/us/en/platform-memory/ddr3-rdimm-snb-ep-memory-list-111014.html

However, the Socket 2011 Xeon boards and CPUs may be above your price range, if you can live with 16GB of unbuffered DDR3 I would go with a Xeon E3-1230 or wait for the Ivy Bridge Xeon variants to to release.
Click to expand...

I have checked out Socket 2011 and the MoBo/CPU combination seems to be out of my price range.

Any justifiable performance gain over the Socket 1155 E3 line other then the fact to get reasonably priced 8GB ram modules?

Any idea when the Ivy Bridge will be coming out?

Thanks a lot for your input!!
 
If your work utilized gpu function and you had a bigger budget then socket 2011 would work well with multiple gpu's due to all the pcie lanes. In your case it shouldn't make a difference.

No one knows for sure when IB server parts are coming out. Desktop variants look like they will be out before the end of the month. The only actual info released on the IB xeons is by the end of the quarter. Maybe they'll come out with the desktop parts or maybe they'll come out in june.
 
pkkevin said:
The other benefit I realize going with E3 will be the SATA III 6.0 Gb/s port, will this be a noticeble difference between SATA 3.0 Gb/s?
Click to expand...
If you're using SSDs, there is a performance difference between SATA 6.0Gb/s and SATA 3.0Gb/s in the read/write speeds. If you're using regular hard drives, really no difference.
pkkevin said:
Will this combo work well?
Click to expand...
It should.
pkkevin said:
If I were to increase SSD to 256gb or HD to 2TB, any solid recommendations?
Click to expand...
I'd go for the 256GB version of the Crucial m4 series. As for 2TB drives, are you looking for storage or speed? If just storage, I recommend this drive:
$130 - Samsung Spinpoint F4 HD204UI 2TB 5400 RPM SATA 3.0Gb/s Hard Drive

If looking for speed, I recommend this drive:
$178 - Hitachi Deskstar 7K3000 HDS723020BLA642 2TB 7200RPM SATA 6.0Gb/s Hard Drive
 
modulus said:
If your work utilized gpu function and you had a bigger budget then socket 2011 would work well with multiple gpu's due to all the pcie lanes. In your case it shouldn't make a difference.

No one knows for sure when IB server parts are coming out. Desktop variants look like they will be out before the end of the month. The only actual info released on the IB xeons is by the end of the quarter. Maybe they'll come out with the desktop parts or maybe they'll come out in june.
Click to expand...

Yeah, like you said, I don't need GPU computation for now.
And I am pretty sure I am not going to wait for IB...

Thanks for your input!
 
Danny Bui said:
If you're using SSDs, there is a performance difference between SATA 6.0Gb/s and SATA 3.0Gb/s in the read/write speeds. If you're using regular hard drives, really no difference.
Click to expand...

Got it, Thanks!

Danny Bui said:
I'd go for the 256GB version of the Crucial m4 series. As for 2TB drives, are you looking for storage or speed? If just storage, I recommend this drive:
$130 - Samsung Spinpoint F4 HD204UI 2TB 5400 RPM SATA 3.0Gb/s Hard Drive

If looking for speed, I recommend this drive:
$178 - Hitachi Deskstar 7K3000 HDS723020BLA642 2TB 7200RPM SATA 6.0Gb/s Hard Drive
Click to expand...
Thanks for the suggestions!!
I will figure out the storage setup within the budget to maximize my needs

Last question, I probably will get a cheap video card to do dual screen. Any suggestions?
I am thinking about HD6450 http://www.newegg.com/Product/Product.aspx?Item=N82E16814125378

By the way, I have an archaic Nvidia GeForce 7200 GS lying around, is that ever going to work? (just Curious)

Thanks so much for your help!!
 
That 7200GS should work if it has enough outputs for you. If it doesn't, you can always buy that HD 6450.
 
Danny Bui said:
That 7200GS should work if it has enough outputs for you. If it doesn't, you can always buy that HD 6450.
Click to expand...

After careful review, I don't see a PCI-E x16 slot for
SUPERMICRO MBD-X9SCM-O LGA 1155 Intel C204 Micro ATX Intel Xeon E3 Server Motherboard http://www.newegg.com/Product/Product.aspx?Item=N82E16813182254

Is it actually going to work with a normal video card?
will the PCI-E x1 video card work for this motherboard and do dual screen?

or should I be looking at another motherboard?
 
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