Powerful workstation for computational tasks: i9-10980XE + 2x 3080

[neff89]

Hey Everyone,

I am a PhD student doing structural biology and we are planning to buy a new workstation for the lab. We regularly perform large computational tasks which are either parallelized CPU intense calculations or based on CUDA cores.

 

Currently, I had this setup in mind, what do you think about the configuration? We are connected via 10Gbit to our storage servers, so we only need 2 SSDs for a dual boot into CentOS or Windows. I am not sure if 2 GeFore 3080 will fit in the case. I also heard that the first batch of GPUs had some issues, do you know if cards from Asus might also have these issues?

 

Case: be quiet! - Dark Base 900
Case fans: 4x 140mm be quiet! Silent Wings 3
CPU: Intel Core i9-10980XE

CPU cooler: be quiet! Dark Rock Pro 4
Mainboard: ASUS WS X299 SAGE
GPU: 2x ASUS Strix NVIDIA GeForce RTX 3080 10GB
RAM: 4x 32GB DDR4-3000 Corsair Vengeance LPX
SSD: 2x 1TB Samsung 970 EVO Plus
PSU: Corsair AXi Series 1600W
LAN: Intel X710-DA2 10Gbit/s (2x SFP+)
OS: Windows 10 Pro 64 Bit

 

Budget (including currency):  up to 8000 €

Country: Germany

Games, programs or workloads that it will be used for: Scientific computing based on CUDA cores

 

[nick name]

My first concern is availability of the CPU and the GPU.  Can you source those?

[SavageNeo]

gpus will fit, but note that you can not sli 3080's. so if that was your intention get 3090 instead.

 

for cpu intense calculations i would get threadripper instead.

 

[SupaKomputa]

4 minutes ago, neff89 said:

CPU: Intel Core i9-10980XE

No. Don't get this. It's old and not very fast.

Get a Ryzen 3950x (16 cores $750), or Threadripper 3960x (24 cores, $1399) all the way to 3990x (64 cores, $3990)

[SavageNeo]

with up to 8k: 

PCPartPicker Part List

Type	Item	Price
CPU	AMD Threadripper 3970X 3.7 GHz 32-Core Processor	€1835.58 @ Computeruniverse
CPU Cooler	Alphacool Eisbaer Aurora 420 41.8 CFM Liquid CPU Cooler	€155.89 @ Aquatuning
Motherboard	Asus Zenith II Extreme EATX sTRX4 Motherboard	€698.53 @ Amazon Deutschland
Memory	Corsair Vengeance RGB Pro 128 GB (4 x 32 GB) DDR4-3000 CL16 Memory	€564.01 @ Amazon Deutschland
Storage	Sabrent Rocket 4.0 1 TB M.2-2280 NVME Solid State Drive	€189.89 @ Amazon Deutschland
Storage	Sabrent Rocket 4.0 1 TB M.2-2280 NVME Solid State Drive	€189.89 @ Amazon Deutschland
Video Card	Asus GeForce RTX 3090 24 GB STRIX GAMING OC Video Card (2-Way SLI)	€1400.00
Video Card	Asus GeForce RTX 3090 24 GB STRIX GAMING OC Video Card (2-Way SLI)	€1400.00
Case	be quiet! Dark Base Pro 900 Rev. 2 ATX Full Tower Case	€226.69 @ Alternate
Power Supply	Corsair 1600 W 80+ Titanium Certified Fully Modular ATX Power Supply	€400.00
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
	Prices include shipping, taxes, rebates, and discounts
	Total	€7151.68
	Generated by PCPartPicker 2020-10-06 18:42 CEST+0200

 

optimal: (money saved): 

PCPartPicker Part List

Type	Item	Price
CPU	AMD Threadripper 3960X 3.8 GHz 24-Core Processor	€1323.93 @ LK-Webservices
CPU Cooler	Alphacool Eisbaer Aurora 420 41.8 CFM Liquid CPU Cooler	€155.89 @ Aquatuning
Motherboard	Asus Prime TRX40-Pro ATX sTRX4 Motherboard	€398.90 @ Alza
Memory	G.Skill Ripjaws V 128 GB (4 x 32 GB) DDR4-3200 CL16 Memory	€472.85 @ Mindfactory
Storage	Sabrent Rocket Q 1 TB M.2-2280 NVME Solid State Drive	€119.99 @ Amazon Deutschland
Storage	Sabrent Rocket Q 1 TB M.2-2280 NVME Solid State Drive	€119.99 @ Amazon Deutschland
Video Card	Asus GeForce RTX 3090 24 GB STRIX GAMING OC Video Card (2-Way SLI)	€1400.00
Video Card	Asus GeForce RTX 3090 24 GB STRIX GAMING OC Video Card (2-Way SLI)	€1400.00
Case	be quiet! Dark Base Pro 900 Rev. 2 ATX Full Tower Case	€226.69 @ Alternate
Power Supply	Corsair 1600 W 80+ Titanium Certified Fully Modular ATX Power Supply	€400.00
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
Case Fan	be quiet! Silent Wings 3 59.5 CFM 140 mm Fan	€22.80 @ Amazon Deutschland
	Prices include shipping, taxes, rebates, and discounts
	Total	€6109.44
	Generated by PCPartPicker 2020-10-06 18:43 CEST+0200

 

 

 

[Random_Person1234]

You should get threadripper. Also I don't think the 3080 can do SLI.

[Mateyyy]

Before jumping onto the usual "gEt AmD" train, have you specifically researched that your software works better with Intel HEDT? For instance, if it can leverage AVX-512?

 

Regarding the GPU side of things, I'm assuming your workload(s) don't require the GPUs to run in SLI, right? Since the 3080s do not support that functionality.

[SavageNeo]

Just now, Mateyyy said:

Before jumping onto "gEt AmD", have you specifically researched that your software works better with Intel HEDT?

Yeah, he did not specify that. Just " cpu intensive". AMD would make more sense then.

 

[Ashiella]

5 minutes ago, Mateyyy said:

Regarding the GPU side of things, I'm assuming your workload(s) don't require the GPUs to run in SLI, right? Since the 3080s do not support that functionality.

No real workloads care about SLI, at most NVLink if you have the top end cards and you have a very specific case. Most just support mGpu with any of the same cards (Same gen nvidia for example), it just makes the cpu split the workload for it, thats why it also likely needs to be fast (clockspeeds?) This is just speculation from the ai work I do sometimes.

[SupaKomputa]

11 minutes ago, SavageNeo said:

snip...

Just to add the possibility of using Threadripper system:

PCPartPicker Part List

CPU: AMD Threadripper 3990X 2.9 GHz 64-Core Processor  (€3645.40 @ Amazon Deutschland) 
CPU Cooler: Alphacool Eisbaer Aurora 420 41.8 CFM Liquid CPU Cooler  (€155.89 @ Aquatuning) 
Motherboard: Asus Prime TRX40-Pro ATX sTRX4 Motherboard  (€398.90 @ Alza) 
Memory: Corsair Vengeance RGB Pro 256 GB (8 x 32 GB) DDR4-3200 CL16 Memory  (€1215.79 @ Alternate) 
Storage: Sabrent Rocket 4.0 1 TB M.2-2280 NVME Solid State Drive  (€189.89 @ Amazon Deutschland) 
Storage: Sabrent Rocket 4.0 1 TB M.2-2280 NVME Solid State Drive  (€189.89 @ Amazon Deutschland) 
Video Card: Asus GeForce RTX 3090 24 GB STRIX GAMING OC Video Card (2-Way SLI)  (€1400.00) 
Video Card: Asus GeForce RTX 3090 24 GB STRIX GAMING OC Video Card (2-Way SLI)  (€1400.00) 
Case: be quiet! Dark Base Pro 900 Rev. 2 ATX Full Tower Case  (€226.69 @ Alternate) 
Power Supply: Corsair 1600 W 80+ Titanium Certified Fully Modular ATX Power Supply  (€400.00) 
Case Fan: be quiet! Silent Wings 3 59.5 CFM 140 mm Fan  (€22.80 @ Amazon Deutschland) 
Case Fan: be quiet! Silent Wings 3 59.5 CFM 140 mm Fan  (€22.80 @ Amazon Deutschland) 
Case Fan: be quiet! Silent Wings 3 59.5 CFM 140 mm Fan  (€22.80 @ Amazon Deutschland) 
Case Fan: be quiet! Silent Wings 3 59.5 CFM 140 mm Fan  (€22.80 @ Amazon Deutschland) 
Total: €9313.65
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2020-10-06 18:54 CEST+0200

 

Just a shy 1300 euro from your budget, you'll get a monster 64 cores, 128 threads and 256gb memory.

[Mateyyy]

7 minutes ago, SupaKomputa said:

-snip-

Just a shy 1300 euro from your budget, you'll get a monster 64 cores, 128 threads and 256gb memory.

What's the point in spending more than double on 3090s, for just 20% more CUDA cores?

Also, "just" a shy €1300..?

[Guest]

This is a mess.

OP, when you return please give as much detail as you can about your workload so that it's not a bunch of shots in the dark.

[SupaKomputa]

2 minutes ago, Mateyyy said:

What's the point in spending more than double on 3090s, for just 20% more CUDA cores?

Also, "just" a shy €1300..?

It support NVLINK.

1300 is just 15% more expensive ---> for double the performance.

[Mateyyy]

7 minutes ago, SupaKomputa said:

It support NVLINK.

..okay? And?

7 minutes ago, SupaKomputa said:

1300 is just 15% more expensive ---> for double the performance.

Oh, I wasn't aware that you already knew exactly what OP's workloads consist of, looked up performance metrics between the 10980XE and 3990X specifically in said workloads and then come to the conclusion that the Threadripper was twice as fast. Same thing with the RAM.

[SupaKomputa]

49 minutes ago, neff89 said:

I am a PhD student doing structural biology and we are planning to buy a new workstation for the lab. We regularly perform large computational tasks which are either parallelized CPU intense calculations or based on CUDA cores.

Parallel computing = Multicores, more cores more performance.

Cuda cores = RTX

1 minute ago, Mateyyy said:

..okay? And?

Oh, I wasn't aware that you already knew exactly what OP's workloads consist of, looked up performance metrics between the 10980XE and 3990X specifically in said workloads and then come to the conclusion that the Threadripper was twice as fast. 

 

[neff89]

Hey everyone,

thanks a lot for for all your comments! So I will try to give a bit more specific details:

 

- For the Graphics cards, indeed we do not need SLI at all. The CUDA cores are used for computational tasks only (unfortunately no gaming  ). Thus I think it makes more sense to go with the 3080, because they have a much better prices/performance.

 

- Most of the CPU intense work is done under Matlab, which is heavily parallelised, so the more cores the better. We already have 5 workstations here (equipped with a ) and they can be connected to a computing cluster in Matlab. As they all have Intel cores, I just have the fear that there are some compatibility issues with Ryzen. I will look into this.

 

- Most of the tasks are quite heavy on RAM, and some of our other workstations with only 64GB RAM run regularly our of memory, so 128GB is minimum and 256GB would certainly be beneficial.

 

- If someone is interested, we are doing Cryo electron tomography and are using subtomogram averaging to resolve protein structures. We are mostly using these software pages:

1.) Reconstruction of tomograms: IMOD: https://bio3d.colorado.edu/imod/ It seems that this would actually run fine with an AMD Ryzen processor. Again, here we can combine our workstations to a computing cluster, and I am not sure if it is fine mixing Intel and AMD

2.) Subtomogram averaging: Dynamo https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Main_Page Which run under Matlab and also is using CUDA cores. I will check if an AMD Ryzen would be compatible with his application.

 

Thanks again for your help

[neff89]

Hey everyone,

here is a small update. We now decided on this setup. What do you think? Thanks again for your feedback!  

 

Case: Fractal Design Define XL R2
Case Fans: be quiet! Silent Wings 3 PWM
PSU: 1500W be quiet! Dark Power Pro P12
Mainboard: ASRock TRX40 Creator
CPU: AMD 3970X
CPU Cooler: Corsair iCUE H150i RGB PRO XT
RAM    128 GB RAM, 4x 32 GB, Corsair Vengeance LPX, DDR4-2666
Graphcis: 2x RTX3080 (Gainward Phoenix)
SSD: 2x 1000GB Samsung 970 EVO Plus
LAN: Intel X710, 10Gbit/s

 

Best,

Steffen