[gmx-users] Parallel running of mdrun

[Dallas B. Warren]

It is one of those forehead slapping days again, d'oh

Previously on this sc did not have to use the mpi on the end, but now  
you do. Problem solved, I think.

  <slap>Yep </slap>

Log file now has nnodes: 2 and there is all the domain decomposition  
details. That is more like it :)

Catch ya,
Dallas Warren

A polar bear is a Cartesian bear that has undergone a polar  
transformation

On 05/02/2009, at 10:36 AM, "Chris Neale" <chris.neale at utoronto.ca>  
wrote:

> I get one line like the following for each core in an mpi job:
> 5723 ?        RL     0:38 /work/cneale/exe/gromacs-4.0.2/exec/bin/ 
> mdrun_mpi -deffnm ./md5_running/s6117B2_md5 -cpt 600
> 5724 ?        RL     0:39 /work/cneale/exe/gromacs-4.0.2/exec/bin/ 
> mdrun_mpi -deffnm ./md5_running/s6117B2_md5 -cpt 600
> ...
>
> And you mean mdrun_mpi right?
>
> Chris.
>
> -- original message --
>
>
> I must be missing something here.  Now we don't need to use the -np   
> switch for grompp or mdrun, you simply specify with mpirun (4.0.3) eg
>
> mpirun -np 4 mdrun -deffnm md_01
>
> Doing that I end up with four separate processes.  Does that mean  
> that  the mdrun being used is not mpi enabled?
>
> This is on a super computer system not compiled by myself.
>
> Catch ya,
> Dr Dallas Warren
>
> A polar bear is a Cartesian bear that has undergone a polar   
> transformation
>
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