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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
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Received on Thu Aug 06 2020 - 00:00:02 PDT
