[gmx-users] Parallel run on a Quad Core

[Justin A. Lemkul]

Chitrita Dutta Roy wrote:
> I tried that way it basically creates 4 jobs and takes hold of 4 cpus 
> but the problem is that it shows to take more time than it would 
> normally without mpirun..and not only that a weird thing starts 
> happening.Once being progressed to some steps it retreats back again to 
> an older one and sometimes it just loops around in that fashion 
> calculating practically the same set of steps over and over again.
> 
> I somehow feel that the tpr file which is needed for the mdrun was not 
> built properly to run on 4 separate cores simultaneously.ANd that is why 
> maybe actually the 4 cores are running the same copy of the program and 
> so the same steps.And what i see is kinda race condition.I guess i 
> compiled it properly with mpi so..now i am helpless.
> 
> Thanks for your help.Waiting for some more.

Please post the following information:

1. The exact series of commands you gave when installing Gromacs.
2. The exact commands you are issuing to create your job (grompp and mdrun).

-Justin

> 
> On Sun, Dec 21, 2008 at 7:56 PM, Manik Mayur <manik.mayur at gmail.com 
> <mailto:manik.mayur at gmail.com>> wrote:
> 
>     On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy <chitrita.md
>     <http://chitrita.md>@gmail.com <http://gmail.com>> wrote:
> 
>         Thanks to all for helping me previously.
>         Now i am unable to arrange the .tpr file for position restraint
>         mdrun on a quad core as in version 4.0.2 grompp -np is not a
>         valid comand can anybody help me in building a tpr file for
>         parallel run on 4 cores of a quad core machine .I have installed
>         gromacs using Open MPI Library and my files are suffixed as _mpi.
> 
>      
>     try running: mpirun -np 4 mdrun_mpi options
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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