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-- Sangeetha On Fri, Aug 12, 2011 at 5:59 AM, Ross Walker <ross.rosswalker.co.uk> wrote: > 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 > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 11 2011 - 21:30:02 PDT