From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Tue Oct 04 2022 - 04:44:45 CDT
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> 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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