You should rerun your test at least 20 times in a row and compare the final
data. Three times isn't enough. If you get a variation, then try a smaller
sized system. GPUs ought to be tested for memory errors every year of use
at minimum. Are you aware of Dr. Ross Walker's gpu validation scripts?
Sincerely,
Dow
⚛Dow Hurst, Research Scientist
340 Sullivan Science Bldg.
Dept. of Chem. and Biochem.
University of North Carolina at Greensboro
PO Box 26170 Greensboro, NC 27402-6170
On Fri, Jun 29, 2018 at 8:02 AM Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Dear Amber users and developers,
>
> I would like to ask you if the GPU testing should be considered successful
> or not.
>
> The purchased GPU was tested on 3 systems - 26, 600 and 1600 thousand
> atoms.
> The NPT runs (pmemd.cuda) after heating with the same seed were performed
> 3 times for each system.
> For each system the numerical results in the mdout files were identical,
> but in one case the simulation of the biggest system stopped after 3 steps
> with message
> "cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> encountered".
> The message
> "Note: The following floating-point exceptions are signalling:
> IEEE_UNDERFLOW_FLAG IEEE_DENORMAL" also occured every time.
> The NPT/pmemd.cuda simulations followed NVT heating and NPT initial
> equilibration with pmemd.MPI.
> The mdin file:
>
> Equil_density_NPT
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 0.1, ig=200000,
> cut = 9.0, ntr = 1,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln=1.0, nscm=5000,
> nstlim = 600000, dt = 0.002,
> ntpr = 1000, ntwx = 1000, ntwr = 10000,
> ioutfm=1, iwrap=1,
> restraintmask='!:WAT & !.H= & !:NA',
> restraint_wt=100.0,
> /
>
> [nstlim number actually varied for each system].
>
> Kind regards,
> Nick
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>
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Received on Fri Jun 29 2018 - 11:30:03 PDT
