Hi all,
While running a NPT equilibration in GPU, I am getting the following error:
NetCDF error: NetCDF: Not a valid ID
at write forces
NetCDF error: NetCDF: Not a valid ID
at write forces
NetCDF error: NetCDF: Not a valid ID
at write forces
.
.
.
My .mdin is:
A NPT simulation for Equilibrium simulations
&cntrl
imin=0, irest=1, ntx=5, ntb=2,
ntt=3, gamma_ln=1.0, tautp=0.5, temp0=310,
cut=12.0, fswitch=10.0,
nstlim=5000000, dt=0.002,
ntc=2, ntf=2,
ntpr=10000, ntwx=10000, ntwr=100000, ntwv=10000, ntwf=10000, ntxo=2,
ioutfm=1,
iwrap=1,
barostat=1, ntp=1, pres0=1.0,
watnam='WAT', owtnm='O',
/
&ewald
vdwmeth = 0,
/
And I am running the command:
mpirun --bind-to none -np 2 $AMBERHOME/pmemd.cuda.MPI -O -i
step5.4_equil-NPT.mdin -p step3_charmm2amber.parm7 -c step5.3_equil.rst -r
step5.4_equil-NPT.rst -o step5.4_equil-NPT.out -x step5.4_equil-NPT.nc
It seems that ntwf is giving the error. I removed this option and then no
error message was displayed.
There was no error message while running the same in a normal CPU machine
(pmemd.MPI)
What could be the reason of such an error?
--
*MIDHUN K MADHU*
Ph.D Student
Dept. of Biological Sciences
IISER Bhopal
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Received on Mon May 14 2018 - 14:30:03 PDT
