From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Tue Oct 25 2022 - 10:14:54 CDT
Hello Daipayan,
If I try to run the simulation with fixedAtoms on I get the following error
FATAL ERROR: CUDASOA integration is incompatible with the following options:
minimization; pressure profiling; Berendsen pressure;
multigrator; Lowe-Andersen; fixed atoms; GBIS; LCPO;
zero momentum; TCL forces; Colvars;
temperature coupling, rescaling, or reassignment;
water models other than TIP3; lonepairs or Drude.
On Tue, Oct 25, 2022, 5:09 PM Daipayan Sarkar <sdaipayan_at_gmail.com> wrote:
> Please provide more context. What is the error message you see in the NAMD
> log?
>
>
>
> -Daipayan
>
>
>
> *From: *Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com>
> *Date: *Tuesday, October 25, 2022 at 8:43 AM
> *To: *Daipayan Sarkar <sdaipayan_at_gmail.com>
> *Cc: *"namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, René Hafner TUK <
> hamburge_at_physik.uni-kl.de>
> *Subject: *Re: namd-l: Query regarding performance
>
>
>
> Hello Daipayan,
>
>
>
> Thanks for the message. Yes now it shows ns/day. But I have another little
> problem. I have fixedAtoms on in my file and namd3 doesn't work with it
> when I try to run. I thought there might be something else in the user
> guide. But namd3 user guide also shows there is fixedAtoms parameter.
> Kindly let me know how to do this.
>
>
>
> P.S. it works with extraBonds but not fixedAtoms
>
>
>
> Thanks
>
>
>
> On Tue, Oct 25, 2022, 12:16 PM Daipayan Sarkar <sdaipayan_at_gmail.com>
> wrote:
>
> Hi Nicholus,
>
>
>
> Do you have “CUDASOAintegrate on” in your NAMD configuration script? Same
> applies for the keyword margin, check
> https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/
>
> I say this because of you mentioned in your email that namd3 log gives you
> “0.030 days/ns”. Usually, the benchmark lines in namd3 log would be in
> “ns/day”. Please check and confirm if CUDASOAintegrate is turned on. Also,
> it seems like your system is minimized and you can perform equilibration
> dynamics using minimization output. So, when using NAMD3, comment out
> minimize in your NAMD configuration script.
>
>
>
> In addition, please follow the steps listed here under section getting
> good performance with NAMD v3 (
> https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!7JOk_L4bH_uAnEUOXcED809rHL3jt7GsdjGiBGTyy7cr-6AJET1WZYr2rSs6cemq5pWTie8qqi-GovHbHkLqltF-GhUH$ ).
> Note, the performance here is reported when benchmarking on A100 GPUs and
> will be different when using V100 GPUs for a similar system size, but I
> expect it to get better than what you currently have.
>
>
>
> -Daipayan
>
>
>
> *From: *Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com>
> *Date: *Tuesday, October 25, 2022 at 4:21 AM
> *To: *Daipayan Sarkar <sdaipayan_at_gmail.com>
> *Cc: *"namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, René Hafner TUK <
> hamburge_at_physik.uni-kl.de>
> *Subject: *Re: namd-l: Query regarding performance
>
>
>
> Hello Rene and Daipayan,
>
>
>
> I am now using namd3. The system is little bigger 85k instead of 80k
> earlier. Also I have change the following parameters
>
>
>
> Timestep 2 (it was 1 earlier)
>
> Cutoff. 12 (it was 14)
>
> Pairlistdist. 14 (it was 16)
>
> fullElectFrequency 2 (it was 4)
>
>
>
>
>
> The benchmark time in the logfile is showing around 0.030 days/ns which
> should have given me around 32 ns per day. This value for the earlier
> simulation with namd2 was around 0.080 days/ns.
>
>
>
> However, both the simulations are giving me around 12 ns per day.
> Considering the benchmark time value for earlier simulation it makes sense.
> But I don't understand why I am getting the same for my current simulation.
>
>
>
> Kindly let me know if I am doing something wrong.
>
>
>
> Thank you
>
>
>
> Regards
>
>
>
> On Tue, Oct 4, 2022, 1:46 PM Daipayan Sarkar <sdaipayan_at_gmail.com> wrote:
>
> 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>
> 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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