Hi,

Please check out
http://manual.gromacs.org/documentation/2016.1/user-guide/mdrun-performance.html.
Your first sample command is woefully inefficient, but for em this likely
doesn't matter.

Mark

On Fri, 2 Dec 2016 09:01 abhisek Mondal <abhisek.m...@gmail.com> wrote:

> 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, <jkrie...@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*
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