From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Tue Oct 04 2022 - 04:07:28 CDT
Hello Rene,
Thanks for the reply. It seems to be a huge difference.
I am using the following for 80k system
namd 2.14 multicore cuda
CPU 32 Xeon 6242
GPU Nvidia Tesla p40 (x1)
Timestep 1fs
What do you mean by nonbeval,fullelecteval
Is it
nonbindedFreq 1
fullElectFrequency 4
I am getting 12.5 ns/day
With increasing the timestep to 2 I can get around 25 ns/day. But still
less than what you mentioned.
Please let me know.
Thanks
On Tue, Oct 4, 2022, 10:45 AM René Hafner TUK <hamburge_at_physik.uni-kl.de>
wrote:
> Hi Nicholus,
>
> this depends on:
>
> - exact NAMD Version (2.x or 3.alphaY)
> - GPU type
> - CPU type
> - timestepping scheme
> - atom number
>
> example one on a cluster I have access to:
>
> - using NAMD2.14 multicore CUDA (but selfcompiled)
> - GPU: 1xV100
> - CPU: 24xCores on XEON_SP_6126
> - timestep,nonbeval,fullelecteval: 2-1-2
> - with ~80k atoms
>
> *Results in: ~56ns/day (averaged value over multiple runs)*
>
>
> Though there may be space to tweak for you (cannot compare without knowing
> your GPU and namd version).
>
> Depending on the system, simulation features you need and quantities
> you're interested in you may try out HMR (
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2019-2020/0735.html)
> and/or NAMD3 (https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ ).
>
> Cheers
>
> René
>
>
>
> On 10/3/2022 10:13 AM, Nicholus Bhattacharjee wrote:
>
> Hello everyone,
>
> I am running a system of around 80k atoms with namd cuda. I am using 32
> CPUs with 1 GPU. I am getting a performance of around 12.5 ns/day. I would
> like to know if this is fine or I am getting a bad performance.
>
> Thank you in advance.
>
> Regards
>
> --
> --
> Dipl.-Phys. René Hafner
> TU Kaiserslautern
> Germany
>
>
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