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

[Justin A. Lemkul]

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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