Thank you for the information.
Unfortunately I was using Amber16. Does the same problem occur in Amber16?
> -----Original Messages-----
> From: "David Cerutti" <dscerutti.gmail.com>
> Sent Time: 2020-08-04 12:40:51 (Tuesday)
> To: "AMBER Mailing List" <amber.ambermd.org>
> Cc:
> Subject: Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks.
>
> This is a known problem in Amber20, which has yet to be fixed pending some
> other developments in the master branch. We know the solution, but the
> release version for now is taking precautions that will only become
> necessary in CUDA11 and later. There is nothing wrong with the code, but
> we are still deliberating what patch to make.
>
> Dave
>
>
> On Sun, Aug 2, 2020 at 11:22 PM 李奕言 <liyiyan.pku.edu.cn> wrote:
>
> > Dear all,
> >
> >
> >
> >
> > Here is a new Amber user, who has been doing MD simulations on GTX 1080 Ti
> > using pmemd.cuda in Amber 16 and have encountered considerable reduction in
> > performance.
> >
> >
> >
> >
> > First I ran the benchmark sets of AMBER 16 GPU acceleration. For NPT
> > simulation of Factor IX with 90,906 atoms, I have got ~89 ns/day on single
> > GPU, slightly less than the benchmark performance (92.08 ns/day), which is
> > acceptable. Since the benchmark results were OK, I was not suspecting any
> > problem with the GPU.
> >
> > When it came to my membrane protein system, which contains a GPCR dimer
> > protein (ffSB14), POPC lipids (lipid 14), waters (TIP3P) and ions, and has
> > a fairly similar atom number of 95,096, I was getting ~65 ns/day on single
> > GPU. This was not what I was expecting, seeing that 95,096 was not THAT
> > larger than 90,906.
> >
> > My input file for the NPT simulation is as follows. I have tried to get
> > as close as possible to the benchmark input.
> >
> > NPT Production Run
> >
> > &cntrl
> > nstlim=250000000, dt=0.002, ntx=5, irest=1, ntpr=50000, ntwr=50000000,
> > ntwx=50000,
> > temp0=300.0, ntt=1, tautp=10.0,
> > ntb=2, ntp=1, barostat=2,
> > ntc=2, ntf=2,
> > ioutfm=1,
> > &end
> > /
> > 1/ I have even cut down the writing of output and trajectories for better
> > performance by raising ntpr and ntwx values, at the cost of inadequate
> > trajectory snapshots. Is this necessary?
> >
> > 2/ Also, currently I am running an aMD simulation with similar input
> > settings, which resulted in ~42 ns/day. Is aMD performance destined to
> > drop compared to conventional MD?
> >
> > Production Run with Accelerated MD
> > &cntrl
> > nstlim=250000000, dt=0.002, ntx=5, irest=1, ntpr=1000, ntwr=50000000,
> > ntwx=1000, ntwprt=8873,
> > temp0=300.0, ntt=1, tautp=10.0,
> > ntb=2, ntp=1, barostat=2, cut=10.0,
> > ntc=2, ntf=2,
> > ioutfm=1,
> > iamd=3,
> > ethreshd=23916, alphad=1104,
> > ethreshp=-187677, alphap=19011,
> > &end
> > /
> >
> > 3/ Does the performance of pmemd.cuda differ among systems, or does it
> > simply depend on the atom number?
> >
> >
> >
> >
> > I am hoping to get tips for improving the performance of my NPT runs.
> >
> >
> >
> >
> > Many thanks for any reply.
> >
> >
> >
> >
> > Best regards,
> >
> > Ian
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Aug 05 2020 - 19:00:02 PDT
