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

[cesteban at unsl.edu.ar]

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
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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