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Suggestions for LGA2011 build

Feb 25, 2012
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#1
Can anyone suggest some parts for an LGA 2011 build. I have an 1155 3770k ivyb for home and love it, but I need a heavy duty computer to number crunch for work so I want to go with 2011 and a 3930k and at least 16gb fast memory. Also, since this is not for gaming, I don't need an amazing gpu so something 100-$150 will suffice for running the occasional photoshop/corel draw on the side. My budget is $2000 with 10% spread and will be buying parts from newegg. I also want to overclock a bit, so worry free liquid cooling such as the h100 seems appealing to me personally, but I am always open to any differing opinions as many of you guys on the forum typically are the experts. Another thing is that I want to run a RAID1 and use the computer to store some data safely, so I need two ITB hdds. I am reusing just one part,a 64gb SSD for a boot drive and I will be making the build next month~ish. Any advice is greatly appreciated~ Thanks in advance!



A side note (read if you want)


Some you you may remember I asked for an lga 2011 build suggestion on the forum a few months back, and I did build it with a 6 core 2.3ghz Xeon and it's chugging along smoothly (abour 2.5x faster than the seven year computer it replaced) However, for kicks when I compared it to my 4 core ivyb build (which was much cheaper if I may add) at home I found out the 2011 build was about 25% slower in my calculations software? The only difference is that the ivyb build is 4 cores and runs at 3.8ghz(turbo) with 16gb ddr3 1600memory, and the 6 core xeon is running at 2.8ghz (turbo) with 16gb ddr3 1333. Is this result normal or expected??? The software uses all physical cores on the processor, but no hyperthreading, so the hex core seemed like it definitely had the advantage despite lower clockspeed...
 
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mfenn

Elite Member
Super Moderator
Jan 17, 2010
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#2
Your 6-core Xeon sounds like an E5-2630, which will actually only turbo up to 2.6 GHz with all 6 cores loaded. Your Ivy Bridge processor sounds like an i5 3570(K), which would normally run at 3.6 GHz with all 4 cores enabled, but many Z77 motherboards use a variation of "Multi-Core Enhancement" which runs the processor at max turbo no matter how many cores are in use. Thus:

2.6 x 6 = 15.6 GHz
3.8 x 4 = 15.2 GHz

Add it the minor architectural improvements in Ivy Bridge and the fact that most applications don't scale perfectly, and it is definitely believable that the quad-core Ivy Bridge would be faster.

As for your new build, I have a few questions:
- Can you tell me a little more about your application?
- Does memory integrity matter to you, or does your application do some of its own verification/validation of results?
- Is your application memory or I/O intensive?
 
Feb 25, 2012
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#3
Your 6-core Xeon sounds like an E5-2630, which will actually only turbo up to 2.6 GHz with all 6 cores loaded. Your Ivy Bridge processor sounds like an i5 3570(K), which would normally run at 3.6 GHz with all 4 cores enabled, but many Z77 motherboards use a variation of "Multi-Core Enhancement" which runs the processor at max turbo no matter how many cores are in use. Thus:

2.6 x 6 = 15.6 GHz
3.8 x 4 = 15.2 GHz

Add it the minor architectural improvements in Ivy Bridge and the fact that most applications don't scale perfectly, and it is definitely believable that the quad-core Ivy Bridge would be faster.

As for your new build, I have a few questions:
- Can you tell me a little more about your application?
- Does memory integrity matter to you, or does your application do some of its own verification/validation of results?
- Is your application memory or I/O intensive?
Thanks for the clarification.

You are correct about the Xeon being the E5 2630. The ivyb processor however is the i7 3770k(which further supports your claim) which for some reason never hits the advertised 3.9 mark (not OCed). The program I am running is Gaussian 09 64bit a quantum chemistry/physics program which essential does a ton of complex math. I have e-mailed the customer support about the program and they say pretty obvious things....more clock speed, faster memory and more cores will speed up calculations. Also they say hyper threading is not supported by the software, so it only uses physical cores.Before starting a calculation, Gaussian allows the user to allocate resources for the job( ie, number of cores, gb ram) In terms of memory usage, in my experience a Gaussian calculation (by itself/ not including OS and multitasking) can use anywhere from 2gb to 6gb of ram, so my total memory useage in Windows 7 can get up to about 10gb in task manager (this may help determine I/O intensity). Gaussian also says that ECC memory is not required by the software.
 
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Feb 25, 2012
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#4
Edit:

I will actually not be needing RAID1 on the build since am planning to use my external hardrive+router to back up. So a single hard drive will suffice.
 

Insert_Nickname

Diamond Member
May 6, 2012
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#5
Also hyper threading is not supported by the software, so it only uses physical cores.
HT should be completely transparent to any software you run from within an operating system. A core with HT gets treated like two physical cores...:confused:

If you need -serious- number crunching, definitely get the 3930K and as much RAM as you can squeeze in. The 3930K gives you almost a full GHz compared with the E5-2630...

Unless you require ECC RAM, then a Xeon is your only choice...

If you use your machine for serious work DO NOT over clock, that can not be stressed enough.

Oh, and if you just need to get a picture on a screen, even a lowly HD5450 (preferably with a displayport) will suffice...
 
Feb 25, 2012
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Thank you for the suggestions.

HT should be completely transparent to any software you run from within an operating system. A core with HT gets treated like two physical cores...:confused:
The HT not being supported is what the software manufacturer told me. Actually they said, "performance gains from HT are negligible for all practical purposes". so I'm just taking their word for it.
 
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mfenn

Elite Member
Super Moderator
Jan 17, 2010
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#7
Ah Gaussian. I am fortunately (unfortunately?) quite familiar with that code. You are absolutely correct that HT provides no benefit and can even degrade performance. Whatever processor you end up going with, make sure to disable HT in the BIOS. I would also absolutely under no circumstances overclock a machine that is running Gaussian calculations, especially not if I was going to publish those results. The whole point of putting up with the horrendous pig of a code that is Gaussian is that your results are certified to be correct by Gaussian, Inc. Run on an unsupported processor configuration and all that goes out the window.

What size of RWF files do you normally see? Gaussian can be quite I/O bound at time, so if your RWF will fit on an SSD, we should definitely go that route.

Also, Gaussian does indeed have extensive error checking routines built in, but it really sucks to get several days into a calculation and see the program abort due to a memory error. :(

Gaussian is a serious program meant for doing serious work, so here's a serious build:

E5-2640 $900 - slightly better than what you have at work
Hyper 212 EVO $31 - just something to keep it quiet while at load
SuperMicro X9SRA $290
Kingston DDR3 1333 ECC 32GB $296
GeForce 210 $23
Samsung 830 256GB $160 AP
Hitachi 7K1000.D $80
Seasonic S12II 430W $60
Antec Eleven Hundred $100
Total: $1940 AR AP
 
Feb 25, 2012
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#8
Ah Gaussian. I am fortunately (unfortunately?) quite familiar with that code. You are absolutely correct that HT provides no benefit and can even degrade performance. Whatever processor you end up going with, make sure to disable HT in the BIOS. I would also absolutely under no circumstances overclock a machine that is running Gaussian calculations, especially not if I was going to publish those results. The whole point of putting up with the horrendous pig of a code that is Gaussian is that your results are certified to be correct by Gaussian, Inc. Run on an unsupported processor configuration and all that goes out the window.

What size of RWF files do you normally see? Gaussian can be quite I/O bound at time, so if your RWF will fit on an SSD, we should definitely go that route.

Also, Gaussian does indeed have extensive error checking routines built in, but it really sucks to get several days into a calculation and see the program abort due to a memory error. :(

Gaussian is a serious program meant for doing serious work, so here's a serious build:

E5-2640 $900 - slightly better than what you have at work
Hyper 212 EVO $31 - just something to keep it quiet while at load
SuperMicro X9SRA $290
Kingston DDR3 1333 ECC 32GB $296
GeForce 210 $23
Samsung 830 256GB $160 AP
Hitachi 7K1000.D $80
Seasonic S12II 430W $60
Antec Eleven Hundred $100
Total: $1940 AR AP
Thank you very much for your input mfenn.

I didn't know about disabling HT :)

RWF files are strange. While Gaussian runs, the files take up like 2-8gb scratch space temporarily (Gaussian allocates it just in case???), but after completion of the jobs, it usually ends up being much less, like 50mb?

Also, is there any need for ecc memory because you just said Gaussian has error checking code? I am actually trying to build this rig for raw speed and will run for short term jobs (jobs that take no more than 12-24hours), to see if certain calculations are plausible, before committing time to run higher level/ more accurate jobs. I already have 2 other systems that do higher level calculations with ecc memory, that run for weeks (where I assume errors are much more likely). I have colleagues that are running i7 w/ gaussian and are reporting no problems, so I really want to go the 3930k route if possible due to the clock speed and support for ddr3 1600 quad channel. I contacted Gaussian and they said ecc memory is not required, if you purchase good quality modules, from a trusted vendor...What would you suggest as parts If I bought the 3930k?


EDIT: I noticed you put in a 256 Samsung ssd. Do you thing that will help on Gaussian alleviating bottlenecks?
 
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mfenn

Elite Member
Super Moderator
Jan 17, 2010
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#9
Regarding the RWF files, yeah Gaussian does that with them unless you give it a certain option to leave them alone when its finished (can't remember off the top of my head, I try to block out all memory of supporting Gaussian). Putting them on the SSD can definitely help if you want to run a bigger simulation. I'd definitely recommend keeping the SSD since you have the budget and $160 is a really good deal.

As for ECC memory, its purpose for Gaussian runs is to protect from crashes due to memory errors, not to protect from bad results (since Gaussian takes care of that itself). For short runs, there is much less risk in terms of potential amount of work lost, so I can see skipping ECC. To do that, swap in these parts:

i7 3930K $570
ASRock X79 Extreme3 $200
G.Skill DDR3 1333 32GB $136

Really, you have the budget for the 3960X, but its not worth the $500 Intel wants for a couple hundred MHz.
 
Feb 25, 2012
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#10
Thanks for the suggestion. I agree, 3960x over the 3930k is probably throwing away about $400 lol.

One last question, sorry for bugging you again haha.

So should I install Gaussian on the SSD and put rest of stuff on the regular hdd b/c I want enough space for Gaussian data and don't really care about boot times for win7 b/c the computer will be on all the time pretty much. This way I will have a dedicated gaussian drive and make most of that ssd w/o compromising space of windows.

Again, I greatly appreciate the help.
 

Insert_Nickname

Diamond Member
May 6, 2012
3,319
12
126
#11
Ah Gaussian. I am fortunately (unfortunately?) quite familiar with that code. You are absolutely correct that HT provides no benefit and can even degrade performance. Whatever processor you end up going with, make sure to disable HT in the BIOS.
Thanks for the heads-up, duly noted...():)
 

mfenn

Elite Member
Super Moderator
Jan 17, 2010
22,403
0
71
www.mfenn.com
#12
You don't actually even have to install Gaussian itself on the SSD. You just need to make sure that your RWF files are going there. You can do this by adding a few lines to your input file (see http://www.gaussian.com/g_tech/g_ur/m_running_w.htm). That being said, it would be a damn shame to build a machine this expensive and not have the snappiness that goes with having an SSD (boot times are one of the lesser benefits of putting in an SSD). You have enough budget left to get another 128GB or 256GB drive for the OS if you want.
 

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