[gmx-users] parallel processing

[jkrieger at mrc-lmb.cam.ac.uk]

Hi Abhisek,

You would need to use another version of gromacs with mpi rather than
thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You
could then use the following command

mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em

I'm not sure why you are specifying -npme 0 but would suggest you don't do
this and instead let the number of separate pme ranks be set
automatically.

Best wishes
James

> Hi,
>
> I'm running gromacs on a cluster configuration as follows:
> 1 node = 16 cores
>
> I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v
> -deffnm em" command.
>
> How can I be able to run on multiple node (I have 20 nodes available) ?
> "-nt" is not doing good here.
>
>
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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