From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Tue Oct 04 2022 - 06:46:10 CDT
Hi Nicholus,
Just to confirm are you using any collective variables based on your choice of using NAMD 2.14? If not, as Rene suggests, NAMD3 should offer better performance.
-Daipayan
From: "owner-namd-l_at_ks.uiuc.edu" <owner-namd-l_at_ks.uiuc.edu> on behalf of René Hafner TUK <hamburge_at_physik.uni-kl.de>
Reply-To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, René Hafner TUK <hamburge_at_physik.uni-kl.de>
Date: Tuesday, October 4, 2022 at 5:50 AM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Cc: Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com>
Subject: Re: namd-l: Query regarding performance
Multiple timestep scheme:
timestep 2; # timestep of 2fs
nonbondedFreq 1 ; # evaluation of nonbonded interactions in every step
fullElectFrequency 2; # electrostratics only evaluated every 2nd step
The factor of 2 may be explained by the power of the V100 vs. P40 but I have no P40 at hand.
If you want/need to run for a real long time then consider HMR and/or NAMD3 if applicable, see below.
Regards
René
On 10/4/2022 11:07 AM, Nicholus Bhattacharjee wrote:
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<mailto: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 -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany
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