[gmx-users] parallel processing

[abhisek Mondal]

But if I want to run the same job in 4 nodes (available cores= 4*16) then
how would this work ?

On Fri, Dec 2, 2016 at 2:20 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> 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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-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*