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High-end machine for genetic analyses

Last response: in Systems
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January 2, 2013 4:50:30 PM

Hello,
I am about to assemble a machine and was looking for advice / opinion on parts.

The purpose is for memory-intensive computing for a single workstation (I cannot make a cluster at this point).
*The machine needs 64GB of RAM for genetic analyses.
*It needs a low-end GPU for several screens (2-3) and graphic intensive software and animations (but not high-end graphic design applications).
*Also, the HDs need to be in RAID for redundancy (I am thinking RAID 1+0, but might just settle for RAID 1).

In terms of budget, I was thinking of keeping it ~$1800
(already have the monitors and software).

This is what I had in mind:
http://pcpartpicker.com/p/vv0o

Some parts might have become obsolete as I haven't kept up to date in the last few months.
Any input would be much appreciated!


January 2, 2013 4:55:46 PM

Seems like it'd do the job. You have 5 HDDs, is that intentional? I though RAID 10 used 4 - maybe look into RAID5 and use only 3 drives.
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January 2, 2013 6:21:22 PM

The WD Black drives will work great for the RAID setup - I use the same drives. Very reliable, fast and very few issues with them.
January 2, 2013 6:31:05 PM

Thanks for the input, I was going to use Win7 x64 and Linux OS.
As far as I know, both would be able to work with 64GB.

You are right in that the Lian-Li case might be a bit smug with the 4 HD, I have tested the ANTEC 300, and I like it for certain things, however I was looking for a more quiet, better air flow case and Lian Li's are great for this (albeit a bit more pricy!). I will keep looking for a case. Thanks for the input!
January 2, 2013 6:31:34 PM

They might have chosen 5 drives on purpose. When setting a big raid array, it's always beneficial to buy and extra drive or two, so when you need to swap, you are swapping with a similar drive as possible. If in 2 years, one of his drives fails, will he be able to buy a 1TB WD black? Probably not, and mixing drives for RAID can mess things up. Having a brand new one in the box, it's easy to switch to it and have the RAID rebuild itself.


As to the OP, what software are you planning on using? A lot of new software like that is being written to take advantage of CUDA or OpenCL processing on a graphics card, so look into the software and see if a better graphics card for processing is more beneficial to you than more cores on a CPU, etc.
January 2, 2013 6:32:53 PM

Replace the GPU with 7750/7770 - same price, better performance. Also, I'd throw in 3930K if the software you're using is CPU intensive. LGA2011 CPUs don't come with a cooler so you'll need to get one of those too, a Cooler Master Hyper 212 EVO takes the value cake.
January 2, 2013 6:38:49 PM

Windows 7 x64 must be the Professional version or greater:

http://msdn.microsoft.com/en-us/library/windows/desktop...

Home versions only recognize <= 16GB RAM.

Linux OS should be fine.

The ANTEC 300 Two I use for my main rig is whisper quiet - I purchased two extra 120MM fans, and none of the fans run at full speed - keeping the noise levels down.

If price is no object - this case has a 5-bay hot swap built in....

http://www.newegg.com/Product/Product.aspx?Item=N82E168...
January 2, 2013 6:43:46 PM

You can get Windows 8 Pro for $40 until the end of month. You'll have to download and install Consumer/Release Preview first since it's an upgrade, but it's not necessary to have a licence of previous Windows.
Either way, it saves you good $200 you can put towards 3930K instead of 3820
January 2, 2013 6:54:23 PM

Why not get RE drives - they're enterprise drives that are designed for RAID setups.

Also, since you are doing a complicated RAID setup like this, there are two major things I would do:

1) Buy a raid card. It makes a big difference in reliability and speed.

2) Buy a 120 / 128 GB SSD to install the OS and programs off of - the users will be a lot more satisfied with it's speed, and feel like their money was much better spent.
January 2, 2013 7:09:23 PM

RoninTexas:
Glad to hear about the ANTEC 300's, my experience wasn't as great in the past. I will seriously consider this case then, as it does bring down the cost and has the space.

getochkn:
The OS will be the professional version, and provided by the university, no worries there. The software cannot handle CUDA yet, this field hasn't caught up yet!

Soda-88:
Thanks! Will get a CPU cooler; the previous i7 chip I had the cooler was ok (temps were kept low, as I don't overclock). There was an i5 stocked cooler that was a bit noisy, so I should reconsider as you point out. Will the 2930k make that much difference for almost double the price?

DarkSable:
I don't have experience with RE drives - any guidance there?

I will look into a RAID card, suggestions?

The SSD drive (Mushkin in the setup, although now considering a Kingston: http://www.neweggbusiness.com/Product/Product.aspx?Item...
) is for the OS / programs.

Thanks again for the input, I really appreciate it.
January 2, 2013 7:17:40 PM

Soda-88 said:
Replace the GPU with 7750/7770 - same price, better performance. Also, I'd throw in 3930K if the software you're using is CPU intensive. LGA2011 CPUs don't come with a cooler so you'll need to get one of those too, a Cooler Master Hyper 212 EVO takes the value cake.



Is this the GPU you were thinking off? I couldn't find a 2x DVI setup with good reviews under $150.
http://www.neweggbusiness.com/Product/Product.aspx?Item...

Thanks!
January 2, 2013 8:38:11 PM

Soda-88 said:
You can get Windows 8 Pro for $40 until the end of month. You'll have to download and install Consumer/Release Preview first since it's an upgrade, but it's not necessary to have a licence of previous Windows.
Either way, it saves you good $200 you can put towards 3930K instead of 3820



Actually you can get it for $14.99
January 2, 2013 8:50:03 PM

Thanks, I can get Windows for $0 :) 
My main concern now is between the 3930k CPU and a 4-core cpu that I had before, and the video card (7770 vs something else).
I am trying to keep it under $1700 as I also need to get an extra monitor and stand.
Thanks again for all the input!

Best solution

January 2, 2013 9:10:29 PM
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The cpu thing will come down if it's a core dependent program or a clock cycle app that you're running. Depending on how the app is written, some do better with pure speed, faster, the better and a k version of a i5 and a good cooler, you can OC at least 500mhz-1ghz over clock and that will help a lot. If it's a core dependent and will take advantage, than an i7 with the hyperthreading will give more cores, and thus work faster. Again, app will determine the cpu to go with.
January 2, 2013 9:26:25 PM

thanks getochkn,

I think fewer cores but faster (and perhaps OC) is better, as several Aps don't take advantage of the cores.

Perhaps then a i7- 2700k to OC?

January 9, 2013 11:15:21 PM

Best answer selected by selas.
!