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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>
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Received on Mon Aug 03 2020 - 22:00:03 PDT
