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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Received on Fri Jun 29 2018 - 05:00:03 PDT
