Re: FEP with cudaSOAIntegrate in NAMD 3.0alph9

From: Kevin Chan (kevin_at_skblnw.com)
Date: Sat Jun 12 2021 - 08:32:06 CDT

Dear Haochuan,

I apologize for the late reply. Buried with works. A test case can be found at https://urldefense.com/v3/__https://github.com/skblnw/namdsntest__;!!DZ3fjg!raQUYgqg4Bk9IpqXhAkbIWCEi6-p0ug54Hj1fow03chQgRz6HJt-CiZyPBrB_swSFw$ .

Thank you in advance for your time and please let me know if you need more details.

Best,
Kevin

> On 05/26/2021 7:43 AM yjcoshc <yjcoshc_at_gmail.com> wrote:
>
>
>
> 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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