Hi,
Im having problems running TI calculations on old K10 GPUs. About 10% of my
jobs produce after a while NaNs in the output. Before that, the run looks
pretty normal. The bombs are not reproducible, when I run the same set of
ligand perturbations multiple times, its always different perturbations and
different lambda values that fails. The same systems ran fine multiple times
with Amber16.
My setup: Amber18, with all updates installed, RH SL6.8 with Cuda8.0. TI
with softcoremasks, with/without HMR. I only observe the crashes on
K10.G1.8GB or K10.G2.8GB, runs on K40m or K40c or GTX1080 cards seem to be
fine.
Any idea how I could trace the source of the problem? Any known issues I
should be aware of - e.g. some weird combination of input parameters that I
use? For reference, I have attached my mdin file (and please no flames - I
know that my input parameters do not reflect the current state of the art -
but hints for improvement are certainly welcome :-).
Thanks a lot,
Th.
# system in water box, production at 300K NPT
&cntrl
imin=0,
ntx=5, irest=1,
ntpr=1000, ntwx=0, ntwe=0, ntwr=250000, ntwprt=0, ioutfm=1,
iwrap=0,
ntf=1, ntb=2, vdw_cutoff=9.0, es_cutoff=9.0, ntp=1, pres0=1.0,
comp=44.6, taup=1.0,
barostat = 2,
nstlim=2500000, dt=0.004,
ntt=3, ig=-1, temp0=300.0, tautp=1.0, gamma_ln=3,
ntc=2,
ene_avg_sampling=1, logdvdl=1,
icfe=1, clambda= 0.4,
timask1=':1', timask2=':2',
ifsc=1, scbeta=18,
scmask1=':LL1.C9,C10,C11,C12,N7,C13,C14,C15,C16,C17,C18,C19,C20,H7,H8,H9,H10
,H11,H12,H13,H14,H15,H16,H17,H18,',
scmask2=':LL2.C7,C8,N4,C9,C10,C11,C12,C13,C14,C15,C16,C17,C18,H5,H6,H7,H8,H9
,H10,H11,H12,H13,H14,H15,H16,',
ifmbar=1,mbar_states=21,
mbar_lambda=0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45,
0.50,
0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.0
/
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Received on Wed Feb 13 2019 - 04:30:02 PST
