Build Advice PC build for processing scientific data ?

luckycharms

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Hi all,

I'm building a machine with a budget of around $2500. It will be used for processing scientific data, sometimes with large datasets. Single-thread performance is most important, multi-thread second. GPU not so important. I'd like 128GB RAM, and at least one NVME drive. I'll need a second drive in there too. Here's a first stab at a build: https://newegg.io/e3ef401 . I don't know much about the diffs between motherboards, so suggestions there especially welcome. Many thanks in advance!


 

kanewolf

Titan
Moderator
Hi all,

I'm building a machine with a budget of around $2500. It will be used for processing scientific data, sometimes with large datasets. Single-thread performance is most important, multi-thread second. GPU not so important. I'd like 128GB RAM, and at least one NVME drive. I'll need a second drive in there too. Here's a first stab at a build: https://newegg.io/e3ef401 . I don't know much about the diffs between motherboards, so suggestions there especially welcome. Many thanks in advance!


If single thread performance is "most important" then you should look at Intel 12th Gen CPU rather than AMD. And why pick the most multithreaded AMD CPU if threads are not as important?
 
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geofelt

Titan
Some thoughts:

The single thread passmark performance rating of the 5950X is 3498.
The rating for the 5800X is the same, only with 16 threads instead of 32.

For your purposes, the very best would be the Intel I9-12900K with 24 threads and a rating of 4173.
Those processors are in hot demand and command a premium over list:
https://www.newegg.com/intel-core-i9-12900k-core-i9-12th-gen/p/N82E16819118339?quicklink=true

The i7-12700K with 20 threads and a single thread rating is 4173 at half the price:
https://www.newegg.com/intel-core-i7-12700k-core-i7-12th-gen/p/N82E16819118343?quicklink=true

Consider the I5-12600K with 16 threads and a rating of 3946:
https://www.newegg.com/intel-core-i7-12700k-core-i7-12th-gen/p/N82E16819118343?quicklink=true

You will need a Z690 based motherboard.
They come in both DDR4 and DDR5 models.
Considering the massive amount of ram you want, look at DDR4.
DDR4 ram is cheaper and the difference in performance is negligible.
The ram you picked is good, but double check support on the motherboard ram QVL list.

The cpu cooler you picked was inadequate for a 5950X
A good cooler is needed to allow the processor to turbo up for max performance.
Go to the noctua cpu compatibility center to find your best cooler.
https://ncc.noctua.at/cpus
Here is the list for the i9-12900K:
https://ncc.noctua.at/cpus/model/Intel-Core-i9-12900K-1577
A very good pick would be the NH-D15s
LGA1700 requires a different cooler mount from the past.
Current stock will have an included lga1700 mounting kit.
Noctua will send you a free kit if you have an older model.
Or, you can buy one for about $10.

Apparently, some motherboards from ASUS have vrm heat sinks that may interfere with some coolers.
Noctua has a check for that also:
https://ncc.noctua.at/motherboards

The K suffix processors include integrated graphics so you do not need a separate graphics card.

You need a better case to provide more front air intake so your cpu cooler can do it's job.
The fractal design focus g is similarly priced.

Samsung 980 PRO m.2 gen4 is a great pick if your processing includes much sequential reading of the ssd.
That is the benefit of the PRO and gen 4 on a Z690 based motherboard.
If such processing is not needed, a less expensive 980 evo plus would do just fine.

On the Power supply, DO NOT buy a cheap psu.
$40 will not buy you anything good.
The evga BQ is considered tier 4 on this list:

Because you are not using a high powered graphics card, you do not need a very strong psu.
This time of year, seasonic often has sales.
Here is a Seasonic Focus 550w unit with a 10 year warranty:
https://www.newegg.com/seasonic-focus-plus-550-gold-ssr-550fx-550w/p/N82E16817151189?Item=N82E16817151189&quicklink=true
 
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luckycharms

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Thanks for your helpful replies! I'll probably go with an i9 or i7 12x00K with DDR4. I'm confused about what speed DDR4 I should get - lots of opinion but little information out there that I could find. Any thoughts on that?
 

luckycharms

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If single thread performance is "most important" then you should look at Intel 12th Gen CPU rather than AMD. And why pick the most multithreaded AMD CPU if threads are not as important?
Not that threads aren't important. Just that single-threaded is more important than multi. Everything is (usually) a balance...
 

luckycharms

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Not true. Since AMD tends to keep total power lower, a CPU with fewer cores can have higher clock speeds for the same power budget.
I meant, I am not singularly focused on single threaded performance. It is the highest priority, but I will be doing some multi-threaded computation as well.
 

kanewolf

Titan
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I meant, I am not singularly focused on single threaded performance. It is the highest priority, but I will be doing some multi-threaded computation as well.
I was just trying to say that getting the most cores will almost always have lower clock speeds, in addition to the highest cost.
Multithreaded HPC type software is difficult to write with efficiency and more dependent on the memory bandwidth. If you are a MATLAB programmer, you should look at the parallel toolkit. It will allow you to parallelize onto a GPU.
 
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geofelt

Titan
Here is one analysis of ddr5 ram speed scaling.
It is of interest because it includes DDR4 3600 as one of the test items.
For gaming, DDR4 3600 is as good as anything.

In your case, try to find apps in the app section that has the characteristics of your workload.
Then see if there is much difference between DDR5 5600(similar to DDR4 3600 cl16) and higher speed ram.
If you see much difference, only then would faster ddr4 ram be indicated.
The question may be moot since 4000 speed ram is about the fastest ddr4 you can get at 128gb.

As ram gets faster, the latency increases. If you divide speed by latency you can get one figure of merit, that will be about 220(higher is better) for most ram.

Looks like 3600 cl16 would be about right.
 
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LinuxDevice

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Are you using any GPU acceleration, e.g., CUDA or OpenCL? If so, then you should know that GPU RAM size does matter (a lot).

I'm not suggesting you should jump to ECC RAM, but with that much RAM it is quite useful. Price would be a downside, and the CPUs capable using this are often not as fast (e.g., Xeon or Threadripper) without paying a hefty fee. However, you are much more likely to fill that RAM and use it a lot and never have an application fail when RAM has a "hiccup". The reliability with high use of RAM is why ECC is usually used in scientific computing.
 
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geofelt

Titan
The first rule for buying ram is to get enough.
128gb seems like you nailed that.

If your apps are the kind that are memory speed intensive, pay more for fast ram.
But, I think I the sweet spot would be 3600 speed which will likely be cas 18.
 

luckycharms

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ok, thanks. so, no huge difference between DDR4 3600, CL 16 vs CL 18?
also, i was getting a warning with adding 1.45V memory, saying that alder lake wants 1.4V max. Think that's an issue?
 

geofelt

Titan
ok, thanks. so, no huge difference between DDR4 3600, CL 16 vs CL 18?
also, i was getting a warning with adding 1.45V memory, saying that alder lake wants 1.4V max. Think that's an issue?
DDR4 ram that is faster than 2666 is made of better binned chips that can be overclocked to higher speeds.
DDR4 is nominally 1.2v.
3600 speed cas 18 should be 1.35 and cas 16 should be 1.45v.

What counts is your motherboard.
Once you have that, go to a ram web site and access their ram selection app.
Enter your motherboard, and you will get a list of supported kits.
It is harder to manage 4 sticks vs. two.
And, speed and timings may be more difficult at 128gb.

Buy a supported kit.
The motherboard ram qvl list will also have a liat of ram that has been tested initially.
 

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