[gmx-users] mdrun using mpirun

[Kay Gottschalk]

mpirun -np 2 mdrun -np 2 works for me...

On Nov 3, 2004, at 9:45 AM, jianzou wrote:

>> Hi Jianzou,
>> it was a bit unclear for me, but did you use
>> grompp -np 2 ...
>> mpirun -np 2 mdrun_mpi -np 2 ...
>> works for me at least.
>> Best regards,
>> Heikki
>
> Thanks a lot, but I tried this but failed again:(
>
> I've checked some posts here, and wonder that why someone use "mpirun 
> -np 2 mdrun_mpi ...", but you use "mpirun -np 2 mdrun_mpi -np 2". 
> Which should be taken?
>
>
> I wrote bhost for lam as
> 127.0.0.1
> 127.0.0.1
> and run as lamboot -v bhost, grompp -np 2 -v, mpirun -np 2 mdrun_mpi -v
> but got singal 11 error.
>
> I also tried to include the full path for mpirun and mdrun, but it 
> does not work in my case.
>
> I check GROMACS User Manual v3.2 - Appendix A. Technical Details - 
> Appendix A.5 Running GROMACS in parallel, which gives 2 examples
>
> 1. A typical command line looks like
>    % mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30
>   this runs on each of the machines goofus,doofus,fred with 10 
> processes on each.
>
> 2. If you have a single machine with multiple processors you don't 
> have to use the mpirun command, but you can do with an extra option to 
> mdrun:
>    % mdrun -np 8 -s topol -v -N 8
>   In this example MPI reads the first option from the command line. 
> Since mdrun also wants to know the number of processes you have to 
> type it twice.
>
> I tried "mdrun -np 2 -s topol.tpr -v -N 2" like the second example 
> above, got the segmentation error.
>
>
> Could anyone please help me out of this?
>
> Thanks in advance.
>
>
> Regards,
>
> Jian Zou
>
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
Rehovot
Israel
+972-8-934 3639