Ok Ross,
I am using the latest version with all the recent updates.
Here is the detail.
GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 14.0.1
|
| 06/20/2014
Thanks for the helpful suggestion.
On Wed, Apr 1, 2015 at 9:09 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Ok - this matches behavior I have seen on other kepler based systems
> (notably K80s) when running multiple GPUs. My current theory is that one of
> the more recent updates must have broken things. I'll investigate some more
> when I get time. In the meantime I suggest just running single GPU runs.
>
> All the best
> Ross
>
> > On Mar 31, 2015, at 8:32 PM, Himanshu Joshi <himanshuphy87.gmail.com>
> wrote:
> >
> > Hello Ross,
> > I ran the with pmemd.cuda and found it printing correctly.
> > So the problem lies somwhere in pmemd.cuda.MPI.
> >
> > Thanks for the help.
> >
> > On Tue, Mar 31, 2015 at 11:36 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> >
> >> Hi Joshi,
> >>
> >> If you run with just pmemd.cuda instead of cuda.MPI do you see different
> >> behavior?
> >>
> >> All the best
> >> Ross
> >>
> >>> On Mar 31, 2015, at 10:58 AM, Himanshu Joshi <himanshuphy87.gmail.com>
> >> wrote:
> >>>
> >>> Dear Friends,
> >>> I am running pmemd.cuda.MPI (AMBER14) in Tesla K40s gpu cards for an
> >>> explicit water DNA system with SPFP precision model. After running few
> >>> steps sucessfully, I am getting **** for temperature and energy values
> as
> >>> typed below followed by the md input file.
> >>>
> >>>
> >>> NSTEP = 45000 TIME(PS) = 54230.000 TEMP(K) = 300.15 PRESS =
> >>> 0.0
> >>> Etot = -1102980.4479 EKtot = 216143.9219 EPtot =
> >>> -1319124.3698
> >>> BOND = 8297.0959 ANGLE = 17306.9385 DIHED =
> >>> 22929.3885
> >>> 1-4 NB = 8627.8031 1-4 EEL = -71177.7576 VDWAALS =
> >>> 134764.0741
> >>> EELEC = -1439871.9123 EHBOND = 0.0000 RESTRAINT =
> >>> 0.0000
> >>>
> >>
> ------------------------------------------------------------------------------
> >>>
> >>> check COM velocity, temp: NaN NaN(Removed)
> >>>
> >>> NSTEP = 50000 TIME(PS) = 54240.000 TEMP(K) = NaN PRESS =
> >>> 0.0
> >>> Etot = NaN EKtot = NaN EPtot =
> >>> **************
> >>> BOND = 0.0000 ANGLE = 4770613.6638 DIHED =
> >>> 0.0000
> >>> 1-4 NB = ************** 1-4 EEL = ************** VDWAALS =
> >>> **************
> >>> EELEC = ************** EHBOND = 0.0000 RESTRAINT =
> >>> 0.0000
> >>>
> >>
> ------------------------------------------------------------------------------
> >>> Here is my md input file
> >>>
> >>> Production run with constant volume
> >>> &cntrl
> >>> ntx=6, irest=1,
> >>> nmropt=0,
> >>> ntrx=1, ntxo = 2,
> >>> ntpr=5000, ntwx=5000, ntwr=10000,
> >>> ntwv=0,
> >>> ntf=2, ntb=1,
> >>> cut=9.0, nsnb=10,
> >>> nstlim=1000000, nscm=10000,
> >>> t=0.0, dt=0.002,
> >>> ntt=1, tautp=0.5
> >>> ntp=0, pres0=1.0, taup=0.5, comp=44.6
> >>> tempi=300.0, temp0=300.0,
> >>> ipol=0, ntc=2, ioutfm = 1
> >>> /
> >>> &ewald
> >>> /
> >>>
> >>> Though, I am running another NPT run using Langevin dynamics using
> >>> anisotropic pressure coupling and MC barostate with same pmemd.cuda.MPI
> >> and
> >>> it is running fine.
> >>>
> >>> Is it something known problem or I am missing something, please
> comment.
> >>> Thanks in advance for your valuable time.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense
> Matter
> >>> TheoryDepartment of Physics IISc.,Bangalore India 560012*
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> >
> >
> >
> > *With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
> > TheoryDepartment of Physics IISc.,Bangalore India 560012*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 31 2015 - 21:30:02 PDT
