Oh in that case just run the equilibration step using the CPU code and then
set ntr=0 and run the production calculation on the GPU and you should be
good.
Let me know if you see this error when ntr=0.
All the best
Ross
> -----Original Message-----
> From: arikcohen [mailto:arikcohen.ucla.edu]
> Sent: Thursday, August 11, 2011 5:18 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] unspecified launch failure launching kernel
> kCalculateMolecularVirial
>
> The restraints are during the eq. step and are being removed in the
> production run.
>
> Thanks a lot
>
> Arik
> On 8/11/2011 4:06 PM, Ross Walker wrote:
> > Yeap... This is the NTB=2, ntr=1 bug. The fix really is coming soon.
> >
> > As I say for now either do not use restraints (why do you want
> restraints
> > after the equilibration anyway?) or set ntb=1 and run with NVT.
> >
> > All the best
> > Ross
> >
> >> -----Original Message-----
> >> From: arikcohen [mailto:arikcohen.ucla.edu]
> >> Sent: Thursday, August 11, 2011 3:54 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] unspecified launch failure launching kernel
> >> kCalculateMolecularVirial
> >>
> >> Sorry, here is the eq.in
> >>
> >> equilibration run (0 - 2 ns)
> >> &cntrl
> >> imin=0, ! No minimization, plain MD(default)
> >> irest=1, ! restart calculation
> >> ntx=5, ! Read X and V formatted, if ntb> 0 read
> >> box,
> >> use V if irest = 1
> >> ntb=2, ! Use pbc Pressure = const
> >> pres0=1.0, ! Reference pressure
> >> ntp=1, ! constant pressure dynamics
> >> taup=2.0, ! Pressure relaxation time
> >> cut=10, ! Non-bonded interaction cutoff
> >> ntc=2, ! SHAKE: Constrain bonds involving H atoms
> >> ntf=2, ! Typically ntf=ntc enable TIP3P constrain
> >> tempi=300.0, temp0=300.0, ! Initial and final(reference) temperature
> if
> >> ntt>0
> >> ntt=3, ! Switch temperature scaling (3 Use
> Langevin
> >> dynamics)
> >> gamma_ln=1.0, ! Collision frequency for Langevin
> dynamics
> >> nstlim=1000000, dt=.002, ! Number of MD steps and step size(in ps)
> >> ntpr=100, ! Print energy every
> >> ntwx=100, ! Print coor every
> >> ntwr=500, ! Print for restart option every
> >> ntr=1, ! Restrain atoms(cartesian space) using
> >> harmonic potentail
> >> &end
> >> Group input for restrained atoms
> >> 30
> >> RES 1 8
> >> RES 10
> >> RES 12 47
> >> RES 49
> >> RES 51 99
> >> RES 101 126
> >> RES 128 199
> >> RES 201 220
> >> RES 222 248
> >> END
> >> END
> >>
> >> Thanks a lot again,
> >>
> >> Arik
> >>
> >> On 8/11/2011 3:12 PM, Ross Walker wrote:
> >>> Hi Arik,
> >>>
> >>> Please send you input files. I suspect the bug is NPT + restraints
> >> which is
> >>> fixed in our development tree. Just waiting some final testing
> before
> >>> release.
> >>>
> >>> For now you can run NVT and you should be fine.
> >>>
> >>> All the best
> >>> Ross
> >>>
> >>>> -----Original Message-----
> >>>> From: arikcohen [mailto:arikcohen.ucla.edu]
> >>>> Sent: Thursday, August 11, 2011 3:05 PM
> >>>> To: AMBER Mailing List
> >>>> Subject: Re: [AMBER] unspecified launch failure launching kernel
> >>>> kCalculateMolecularVirial
> >>>>
> >>>> No. just a regular enzyme-substrate calculation.
> >>>>
> >>>> Arik
> >>>>
> >>>> On 8/11/2011 3:03 PM, Scott Le Grand wrote:
> >>>>> Organic solvent or lipid bilayer simulation by any chance?
> >>>>> On Aug 11, 2011 2:59 PM, "arikcohen"<arikcohen.ucla.edu>
> wrote:
> >>>>>> Dear Users,
> >>>>>>
> >>>>>> While running on a GPU cluster I encountering from time time the
> >>>>>> following persistent error:
> >>>>>>
> >>>>>> *unspecified launch failure launching kernel
> >>>> kCalculateMolecularVirial*
> >>>>>> I would be most thankful for any help/suggestion you might have.
> >>>>>>
> >>>>>> Thanks,
> >>>>>>
> >>>>>> Arik
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>> _______________________________________________
> >>>> 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
> >>
> >> _______________________________________________
> >> 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
>
>
> _______________________________________________
> 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
Received on Thu Aug 11 2011 - 17:30:03 PDT
