[gmx-users] [Fwd: Please solve my problem]

[cesteban at unsl.edu.ar]

Hi again
the MPI coding is OPEN MPI 1.2.7 that is  found in the ROCKS CLUSTER 5.1
distribution
thanks
Carmen
>
> cesteban at unsl.edu.ar wrote:
>> Hi All
>> I have similar problem using gromacs 4.0.2.
>> The MD simulation (5 ns) on single processor is complited in 5 days, but
>> the same MD can`t be complited on cluster on 4 or 8 processors. The MD
>> simulation is stopped without any error message.
>> Any help would be appreciated
>
> Which MPI implementation are you using?  Some are known to be buggy.
> Also, to
> rule out any other potentially buggy behavior, upgrade to version 4.0.5;
> 4.0.2
> is several months old.
>
> -Justin
>
>> Carmen
>>> To,
>>>        David van der Spoel
>>>
>>> Dear Sir,
>>>
>>> I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a
>>> problem.
>>> I am giving job for 500000 steps step size 0.002ps (total 1ns) but my
>>> job is stopped after 470000 steps. when i run this on 4 processors.
>>>
>>> But the same job is completed on 2 processors.Why this happing i am not
>>> able to understand.
>>>
>>> Another thing is that job for 1500000 steps step size 0.002ps (total
>>> 3ns) is stopped after 375000 steps on 2 processors
>>> and after 587000 steps on 4 processors, without any error message.
>>>
>>> What could be the problem and how to solve it, please help me.
>>>
>>> even i tried the 2 same jobs for 1000000 steps step size 0.002ps (total
>>> 2ns), one on single processor it is completed in 8 days
>>> but the same job is stop after 550000 steps on 4 processors.
>>>
>>> Is there any change is required in MPI coding or in .mdp files. Sir if
>>> you need any other please let me know.
>>>
>>> Please solve my problem, I will be highly obliged.
>>>
>>>
>>> DvdS:
>>>
>>> Please upgrade to a recent version. 3.2.1 is more than five years old.
>>>
>>>
>>>
>>> With warm regards.
>>> Shikhar
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------
>>> Shikhar Gupta
>>> Senior Research Fellow
>>> Pharmacoinformatics Department
>>> Block- A (Room No.- 208)
>>> National Institute of Pharmaceutical Education & Research( NIPER )
>>> Sec- 67, S.A.S Nagar
>>> Mohali, Punjab (India)
>>> Web-Site: www.niper.ac.in <http://www.niper.ac.in>
>>> PIN- 160062
>>> Email:shik_sun at rediffmail.com
>>> <mailto:Email%3Ashik_sun at rediffmail.com>,shiksun at gmail.com
>>> <mailto:shiksun at gmail.com>
>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------
>>> Shikhar Gupta
>>> Senior Research Fellow
>>> Pharmacoinformatics Department
>>> Block- A (Room No.- 208)
>>> National Institute of Pharmaceutical Education & Research( NIPER )
>>> Sec- 67, S.A.S Nagar
>>> Mohali, Punjab (India)
>>> Web-Site: www.niper.ac.in <http://www.niper.ac.in>
>>> PIN- 160062
>>> Email:shik_sun at rediffmail.com
>>> <mailto:Email%3Ashik_sun at rediffmail.com>,shiksun at gmail.com
>>> <mailto:shiksun at gmail.com>
>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>>> University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
>>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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>>
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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