Re: Query regarding performance

From: René Hafner TUK (
Date: Tue Oct 04 2022 - 03:45:24 CDT

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
and/or NAMD3 ( ).



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

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