From: yjcoshc (yjcoshc_at_gmail.com)
Date: Wed May 26 2021 - 06:43:16 CDT
Hi Kevin,
Could you share some test input files for testing and debugging?
Thanks,
Haochuan Chen
On 5/25/21 8:39 AM, Kevin Chan wrote:
> Dear Users,
>
> I am trying to speed up an FEP calculation using /cudaSOAIntegrate
> /with NAMD 3.0alpha9 single-node path, however, failed by getting either
>
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> or
>
> FATAL ERROR: Low global CUDA exclusion count! (116807 vs 116813)
> System unstable or pairlistdist or cutoff too small.
>
> The system has been tested with NAMD2.14 and NAMD3.0alpha9 without
> /cudaSOAIntegrate /and worked perfectly fine.
>
> So I have tried to tackle the errors by
>
> 1. pairlistdist 13.5 to 16
> 2. margin 4, 8, 16, 20
> 3. /LangevinPistonDecay /100 to 1000
>
> None of the combination worked. Sometimes first 1 or 2 windows (lambda
> 0 to 0.001) got finished (500k+ steps), but I never got the middle
> windows (lambda > 0.1) running. I also tried the alpha8 version and
> had the same results. I set stepsPerCycle to 400 and pairlistsPerCycle
> to 40 all the time. The run command is simply "namd3 +p1 +devices 0".
>
> I understand that FEP with CUDA speedup is still in alpha, so any
> experience shared will be greatly appreciated.
>
> Thanks,
> Kevin
> Zhejiang University
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