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

[Earthworm Jim]

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.

[Tristerin]

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.  

 

 

[Chen G]

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.

[Radium_Angel]

32 minutes ago, Earthworm Jim said:

Will there be any issues running Linux

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

[igormp]

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.

[Radium_Angel]

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. 

[igormp]

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.