Agreed, the topology for a membrane system may be denser in terms of atoms
that a protein in water system. If that is the case, the non-bonded
kernels are going to run slower, but there is no way around this. If you
are seeing the benchmarks run at about the right pace then it's your
system. You also have a 10A cutoff in there, versus a 9A used in the
benchmarks.
Dave
On Thu, Aug 6, 2020 at 2:52 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
> It might help more-informed people to mention your topology.
>
> AMBER Cuda is after my time, but I'll go ahead and speculate that the
> nonbonded ops on cuda itself should be the same-ish for any N atoms, but
> that if your topology is off the developers' beaten track, maybe there's
> a bottleneck in collecting the data. What does nvidia-smi say about GPU
> usage?
>
> Bill
>
> (I play cuda for tensorflow.)
>
>
> On 8/5/20 11:43 PM, 李奕言 wrote:
> > Thanks again for your kind reply.
> >
> > As much as I wish to get an upgrade, I am still wondering if there is
> any solution within Amber16.
> > The benchmark tests went well, but the actual system with similar number
> of atoms got much slower -- Is this a general problem in Amber16 that can
> only be fixed in newer versions? Does the performance of pmemd.cuda differ
> among systems, or does it simply depend on the atom number?
> >
> > I would be grateful if you could help.
> >
> >> -----Original Messages-----
> >> From: "David Cerutti" <dscerutti.gmail.com>
> >> Sent Time: 2020-08-06 10:48:36 (Thursday)
> >> To: "AMBER Mailing List" <amber.ambermd.org>
> >> Cc:
> >> Subject: Re: [AMBER] Reduced Performance with pmemd.cuda Compared With
> Benchmarks.
> >>
> >> We made some performance improvements in Amber18 that will carry over to
> >> Amber20 once the patch hits. The sooner you can upgrade, the better,
> but
> >> the performance of Amber20 will probably still be better than Amber16
> on a
> >> GTX-1080Ti even without the patch.
> >>
> >> Dave
> >>
> >>
> >> On Wed, Aug 5, 2020 at 9:59 PM 李奕言 <liyiyan.pku.edu.cn> wrote:
> >>
> >>> 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
> >>>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
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> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> Phobrain.com
>
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Received on Thu Aug 06 2020 - 02:30:02 PDT
