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
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Received on Fri Oct 14 2011 - 15:00:02 PDT
