The simulations do not freeze on different clusters (with 2070s), so
apparently it is something specific to that particular cluster. Is there any
specific programs that Amber would encounter an incompatibility, for
instance during the recording of the output files?
Or is there any way to increase the verbosity of the *out files or mdinfo
file that would help me detect what causes my simulations to lock up??
On Fri, Oct 14, 2011 at 6:15 PM, E. Nihal Korkmaz
<enihalkorkmaz.gmail.com>wrote:
> Unfortunately, it locks up in both 2070 and 480.
>
> I am currently trying same files on a different GPU cluster of 2070s,
> fingers crossed!
>
>
>
> On Fri, Oct 14, 2011 at 5:29 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
>
>> 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
>> >
>> _______________________________________________
>> 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
>
>
>
--
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
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Received on Mon Oct 17 2011 - 14:00:03 PDT
