Re: Setting up GPU workstation advice

From: horacio poblete (
Date: Mon Jan 08 2018 - 07:17:52 CST

Hi Lewis.

I have a very similar setting-up than yours.
I have a 2 x E5-2683 v4, 16C. 2.1GHz (32 cores=64 threads total) plus 2 and 4 GTX 1080Ti.

I have been running on it 24/7 also, without any problem. The only issue is that namd still yet been cpu dependent more than GPU.
example: With one of the servers running 2 calculation simultaneously ( each one: 32 threads +1GPU, ~45K atoms), I can reach ~100 ns/day but but the performance of the GPUs reach only to the ~60% of the GPU.
on the other hand, in the other server, running 4 calculations simultaniously (16 threads +1GPU, each) I can get ~60-for the 70 ns/day but now I am using only the 38% of each CPU.
I dont know if the namd developers are working on improve it, I hope yes!.

right now I am also buying the same configuration than yours (2x20Cores 3.6GHz +2 and 4GPU). Let see if this extra 8 threads improves the performance.


Horacio Poblete Vilches PhD.
Principal Investigator
Center for Bioinformatics and Molecular Simulations
Escuela de Ingeneria en Bioinformática
Universidad de Talca, Chile.
Phone: +56712203041

> On Jan 7, 2018, at 11:28 PM, Lewis Martin <> wrote:
> Hi NAMDers,
> I'm lucky enough to be setting up quite a high end workstation for MD purposes. I want to check here first for any experience or advice available.
> The CPU/GPU setup will look something like this:
> CPUs: 2 x Intel Xeon E5-2673 V4: 20 cores each = 40 cores
> GPUs: 2 x Nvidia GTX Titan Xp
> Alternatively, I can replace each of the Titan Xp GPUs with two GTX 1080 Ti's for the same price, so 4 GPUs total.
> I haven't found any reference to Titan Xp or 1080 Ti on the NAMD mailing list. My system size is not enormous, probably 200-300k atoms, but I expect to be running the workstation 24/7 at times.
> So my question is - if anyone out there has a similar setup, can you see any problems with this workstation?
> Thanks,
> Lewis
> Lambert Initiative
> University of Sydney

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:47 CST