If it doesn't lock up on the 2070, but does on the 480, it is likely
defective HW.
If it locks up on the 2070, and Ross can repro it on his 20xxs, I know what
I'll be doing this weekend :-)...
But shooting from the hip, I'm guessing this is a bad GPU.
On Fri, Oct 14, 2011 at 2:55 PM, Ross Walker <rosscwalker.gmail.com> wrote:
> Can you send me the input files for one of the simulations that locks
> please so I can try to reproduce it.
>
> Does it lock up on both the GTX480 and C2070?
>
> All the best
> Ross
>
>
>
> On Oct 14, 2011, at 15:28, "E. Nihal Korkmaz" <enihalkorkmaz.gmail.com>
> wrote:
>
> > Yes, I applied the bugfix patches during the first configuration of Amber
> on
> > the cluster as directed on the Amber website.
> >
> > Not the exact same point, but always after 500 ns for that particular
> > simulation.
> > I just realized it got locked up for different proteins (shorter) too at
> > around 200 ns. I simulate a series of the same protein for different
> > conditions (T and salt conc), some goes smoothly some gets locked up. I
> > checked the energy logs in the *.out file, nothing seems unusual and
> nothing
> > is drastically different between simulations go smooth and those freeze.
> >
> > Thanks,
> > Nihal
> >
> > On Fri, Oct 14, 2011 at 2:15 PM, Ross Walker <rosscwalker.gmail.com>
> wrote:
> >
> >> There are a lot of unnecessary defaults in your input file. Like
> specifying
> >> taup for a GB run. You can probably also set ntwr much larger to improve
> >> performance. And a gamma_ln of 20 is probably a bit high. None of these
> >> should cause a lockup though.
> >>
> >> Can you confirm that you are running with the latest bugfixes. In
> >> particular bugfix.17 for Amber 11.
> >>
> >> Also does the calculation always lockup at the exact same point?
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>
> >> On Oct 14, 2011, at 14:17, "E. Nihal Korkmaz" <enihalkorkmaz.gmail.com>
> >> wrote:
> >>
> >>> Amber 11, I tried on GeForce GTX 480 and Tesla C2070 processors, on
> Linux
> >>> (CentOS release 5.6). We have Cuda 4 for nvidia compiler. I am running
> >> with
> >>> pmemd.cuda.
> >>>
> >>> and that's my in file below (although same file works ok with the
> >> homologous
> >>> structure) :
> >>> &cntrl
> >>> imin=0,
> >>>
> >>> ntb=0,
> >>> ntx=5,
> >>> irest=1,
> >>>
> >>> ntpr=200,
> >>> ntwr=200,
> >>> ntwx=200,
> >>> ntwe=200,
> >>>
> >>> nstlim=5000000,
> >>> dt=0.002,
> >>>
> >>> ntt=3,
> >>>
> >>> temp0=300,
> >>> tempi=300,
> >>> ig=-1,
> >>> tautp=1,
> >>> gamma_ln=20,
> >>>
> >>> ntp=0,
> >>> pres0=1,
> >>> taup=1,
> >>>
> >>> ntc=2,
> >>> tol=0.00001,
> >>>
> >>> ntf=2,
> >>> ntb=0,
> >>> dielc=1,
> >>> cut=9999,
> >>> rgbmax=12,
> >>> ipol=0,
> >>> ifqnt=0,
> >>> igb=5,
> >>> saltcon=0.15,
> >>> ioutfm=1,
> >>> nscm=100,
> >>> &end
> >>>
> >>>
> >>> On Fri, Oct 14, 2011 at 1:05 PM, Scott Le Grand <varelse2005.gmail.com
> >>> wrote:
> >>>
> >>>> What revision of AMBER? What GPU? What OS? What driver? What
> toolkit
> >> did
> >>>> you compile with?
> >>>>
> >>>>
> >>>>
> >>>> On Fri, Oct 14, 2011 at 10:55 AM, E. Nihal Korkmaz
> >>>> <enihalkorkmaz.gmail.com>wrote:
> >>>>
> >>>>> Dear all,
> >>>>>
> >>>>> I keep having a problem that only for a particular protein the
> >>>> simulation
> >>>>> "freezes" and by freeze I mean, it looks like the job is running but
> no
> >>>>> changes are made on the output files even if you wait 2 days. I am
> >> using
> >>>>> igb=5 on GPU, it is a 114 amino acid long protein, I have the
> >> homologous
> >>>>> structure running (112 amino acid long) without a problem. But that
> >>>>> specific
> >>>>> one stops without being dropped of the queue or any error messages at
> >>>> all.
> >>>>> I
> >>>>> checked the output files, no '*' or 'NaN' are present. I also tried
> >>>> running
> >>>>> on different machines, same thing happens. I tried starting from a
> >>>>> different
> >>>>> restart file, nothing changes. I always freezes although at different
> >>>> time
> >>>>> steps.
> >>>>>
> >>>>> Has anyone have such a problem before? What can be the causes? I'd
> >>>>> appreciate any comments or suggestions.
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> --
> >>>>> Elif Nihal Korkmaz
> >>>>>
> >>>>> Research Assistant
> >>>>> University of Wisconsin - Biophysics
> >>>>> Member of Qiang Cui & Thomas Record Labs
> >>>>> 1101 University Ave, Rm. 8359
> >>>>> Madison, WI 53706
> >>>>> Phone: 608-265-3644
> >>>>> Email: korkmaz.wisc.edu
> >>>>> _______________________________________________
> >>>>> 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
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Elif Nihal Korkmaz
> >>>
> >>> Research Assistant
> >>> University of Wisconsin - Biophysics
> >>> Member of Qiang Cui & Thomas Record Labs
> >>> 1101 University Ave, Rm. 8359
> >>> Madison, WI 53706
> >>> Phone: 608-265-3644
> >>> Email: korkmaz.wisc.edu
> >>> _______________________________________________
> >>> 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
> >>
> >
> >
> >
> > --
> > Elif Nihal Korkmaz
> >
> > Research Assistant
> > University of Wisconsin - Biophysics
> > Member of Qiang Cui & Thomas Record Labs
> > 1101 University Ave, Rm. 8359
> > Madison, WI 53706
> > Phone: 608-265-3644
> > Email: korkmaz.wisc.edu
> > _______________________________________________
> > 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
>
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Received on Fri Oct 14 2011 - 16:00:02 PDT
