[gmx-users] Parallel run on a Quad Core

[Chitrita Dutta Roy]

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.

On Sun, Dec 21, 2008 at 7:56 PM, Manik Mayur <manik.mayur at gmail.com> wrote:

> On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy <chitrita.md at 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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