Jump to content
Search In
  • More options...
Find results that contain...
Find results in...
Earthworm Jim

NON-GAMING BUILD (Scientific) - Building a computer for running molecular dynamics codes (and maybe some computational fluid dynamics).

Recommended Posts

Posted · Original PosterOP

Hi all, 


I Hope you are all remaining reasonably sane during the lockdown. I would like some advice. I want to build a computer for molecular dynamics simulations (CFD capability would also be nice but not required). This is partly for fun, but It also has the potential to make my life a lot easier. I would like to build a machine that can blast through numeric calculations as its primary function. 


My last computer build was a gaming rig I built about 5-6 years ago. But for this machine I basically want the best CPU possible with a budget machine built around it. The software packages I use run calculations in parallel, so for this application a high number of cores/threads is preferable to clock speed (or so I have been told). 


No gaming. No rendering. Just a pure number cruncher. I have been looking at decent CPUs and some are stunningly cheap for what they are. Such as the AMD 1st Gen RYZEN Threadripper 1920X and AMD RYZEN 7 2700 8-Core. I basically would like to build a computer around a good multi-core processor. However, I obviously don’t want to waste money on things like a fancy graphics card etc. if it’s primarily a number cruncher. 

 

  1. Graphics card – Just how cheap can I go with my graphics card. Theoretically I shouldn’t need one? And I am planning on accessing this machine remotely most of the time anyway. Or will I miss out on so called “GPU Acceleration”?
  2. Power Supply – What kind of power supply will I need? can I go quite low? 
  3. Thermals – What kind of cooling will in need, will a fan be ok? or would I need something more substantial?
  4. Will there be any issues running Linux (CentOS 8 ) on this system?


If anyone has suggestions/experience building a rig like this and can give any advice, guidance or suggested resources showing similar builds I could look at would be greatly appreciated. 


Sorry for the long post and thanks.

Link to post
Share on other sites

Is your software limited by the number of threads available?  If not, I would think that the Ryzen 9 3950X would be the best bang for buck at the moment.  

 

 


Workstation Laptop: Dell Precision 7540, Xeon E-2276M, 32gb DDR4, Quadro T2000 GPU, 4k display

Ryzen Rig 2: ASrock B450 Pro4 ATX, Ryzen 7 1700 @ 4.2ghz all core 1.4vCore, AMD R9 Fury X w/ Swiftech KOMODO waterblock, Custom Loop 2x240mm + 1x120mm radiators in push/pull 16gb (2x8) 3600mhz V-Color Skywalker (or 4x8gb DDR4 2666mhz for large tasks), Corsair HX850 PSU, 128gb Patriot Scorch NVMe Win 10 boot drive, 500gb Samsung 840 EVO SSD, CoolerMaster HAF XM Case.  Zalman K600S keyboard, Zalman ZM-GM1 mouse, Hannspree HF207 and Acer AL2016W monitors

https://www.3dmark.com/3dm/37004594?

Ryzen Rig 1: ASUS B350-PRIME ATX, Ryzen 7 1700, Sapphire R9 Fury Tri-X Nitro 4gb HBM, 16gb (2x8) 3200mhz V-Color Skywalker, ANTEC Earthwatts 750w PSU, MasterLiquid Lite 120 AIO cooler in Push/Pull config as rear exhaust, 250gb Samsung 850 Evo SSD, Patriot Burst 240gb SSD, Cougar MX330-X Case.  Zalman K600S keyboard, Zalman ZM-GM1 mouse, Acer XF270HU 2560x1440 144hz IPS monitor

https://www.3dmark.com/3dm/37628874?

Dwight: The Mixed Metals Loop Media Center.  Ask me about it.  Currently decommissioned to move to an mATX setup on a new MOBO once I pick one out (getting its facelift as of June 2020 have new air cooler, drives etc.  About 60% finished.  Will no longer be a closed loop system.

Schrute: ASUS M5A99FX Pro R2.0, FX 8350, Sapphire R9 Fury Tri-X Nitro 4gb HBM, 16gb (4x4) Corsair Vengeance DDR3 1600mhz, Sparkle/FSP 650w PSU, Corsair H100i GTX 240mm AIO w/ 12mm thick fans to fit in top exhaust, 256gb TIMETEC SSD, 1tb WDBlack HDD, Rosewill Nautilus 1.0 case.  DSI 90-Key Mechanical Keyboard w/ Cherry Red switches, Generic mouse, 37" 1080p TV

Micro Form Factor Dell OptiPlex 3040: Dell 0MGK50 A02, i3-6100T, 2x4gb DDR3 1600, Team Group 120gb SSD, 500gb Seagate 7mm HDD attached storage, Windows 10 Pro, Logitech K400+, USB Wifi adapter all vesa mounted to the back of a 37" 1080p TV for form factor in the kitchen

Linux Box: Toshiba Laptop, i7 620M, NVS graphics, 2gb ram tinker toy at the moment.  Running Manjaro at the moment

APU Laptop: I need to clean this things TIM up so it can boot into Windows 7 for more than 5 minute before overheating at idle, it has things, I just haven't been on it in 2 years or so

Link to post
Share on other sites
  1. No idea if what you're doing can be GPU accelerated, but if it can, you could potentially be missing out several folds of performance.
  2. No, you do not want to cheap out on PSU for something that will be running full power for extended periods of time.
  3. A properly designed airflow should be sufficient with just air coolers. Liquid cooling solutions are not economical in terms of performance per dollar.
  4. Not sure, I've heard about some issues with Ryzen and Linux.
Link to post
Share on other sites
8 hours ago, Earthworm Jim said:

Hi all, 


I Hope you are all remaining reasonably sane during the lockdown. I would like some advice. I want to build a computer for molecular dynamics simulations (CFD capability would also be nice but not required). This is partly for fun, but It also has the potential to make my life a lot easier. I would like to build a machine that can blast through numeric calculations as its primary function. 


My last computer build was a gaming rig I built about 5-6 years ago. But for this machine I basically want the best CPU possible with a budget machine built around it. The software packages I use run calculations in parallel, so for this application a high number of cores/threads is preferable to clock speed (or so I have been told). 


No gaming. No rendering. Just a pure number cruncher. I have been looking at decent CPUs and some are stunningly cheap for what they are. Such as the AMD 1st Gen RYZEN Threadripper 1920X and AMD RYZEN 7 2700 8-Core. I basically would like to build a computer around a good multi-core processor. However, I obviously don’t want to waste money on things like a fancy graphics card etc. if it’s primarily a number cruncher. 

 

  1. Graphics card – Just how cheap can I go with my graphics card. Theoretically I shouldn’t need one? And I am planning on accessing this machine remotely most of the time anyway. Or will I miss out on so called “GPU Acceleration”?
  2. Power Supply – What kind of power supply will I need? can I go quite low? 
  3. Thermals – What kind of cooling will in need, will a fan be ok? or would I need something more substantial?
  4. Will there be any issues running Linux (CentOS 8 ) on this system?


If anyone has suggestions/experience building a rig like this and can give any advice, guidance or suggested resources showing similar builds I could look at would be greatly appreciated. 


Sorry for the long post and thanks.

1. You shouldn't need one at all, unless you want to do some kind of rendering of you final simulation to present in a slide or something, then a cheap GPU should me more than enough (a 1050 or a 750, for example)

2. A 550w should be more than enough.

3. A big air cooler should do the trick, like the noctua nh-u14s

4. Most issues have been sorted out already. CentOS 8 probably has everything backported into its kernel.

 

As someone said before, you could give a look at the 3950x or even the newest threadripper lineup.

 

7 hours ago, Radium_Angel said:

Go with Xeons, and there won't be an issue

More expensive and worse performance due to mitigations and older arch.

 

8 hours ago, Chen G said:
  1. No idea if what you're doing can be GPU accelerated, but if it can, you could potentially be missing out several folds of performance.

Most CFD stuff can't be GPU accelerated. And, even when it's possible, it requires a double precision enabled card, which means high-end Teslas, or older Quadros/Titans. Even a K80 smashes a 2080Ti when it comes to FP64.


FX6300 @ 4.2GHz | Gigabyte GA-78LMT-USB3 R2 | Hyper 212x | 3x 8GB + 1x 4GB @ 1600MHz | Gigabyte 2060 Super | Corsair CX650M | LG 43UK6520PSA
ASUS X550LN | i5 4210u | 12GB
Lenovo N23 Yoga

Link to post
Share on other sites
2 hours ago, igormp said:

More expensive and worse performance due to mitigations and older arch.

Which is more important? Absolute compatibility, or bang for the buck? I can't answer that, only the OP can. 


So rise up, all ye lost ones, as one, we'll claw the clouds

Link to post
Share on other sites
3 minutes ago, Radium_Angel said:

Which is more important? Absolute compatibility, or bang for the buck? I can't answer that, only the OP can. 

AMD has both nowadays, unless OP's software makes use of AVX-512. Then I'd say to go with Intel.


FX6300 @ 4.2GHz | Gigabyte GA-78LMT-USB3 R2 | Hyper 212x | 3x 8GB + 1x 4GB @ 1600MHz | Gigabyte 2060 Super | Corsair CX650M | LG 43UK6520PSA
ASUS X550LN | i5 4210u | 12GB
Lenovo N23 Yoga

Link to post
Share on other sites

Create an account or sign in to comment

You need to be a member in order to leave a comment

Create an account

Sign up for a new account in our community. It's easy!

Register a new account

Sign in

Already have an account? Sign in here.

Sign In Now

Newegg

×