[gmx-users] REMD run on higher nodes.

[suhani nagpal]

Sir

Yeah, I meant to use twice the hardware and i have already invoked
mpiexec_mpt.

the pbs script works fine if i start afresh mdrun of the tprs but if i
extend the simulation run by -cpi filename -noappend the run doesnt take
place.




On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Not sure what you're asking, but if you're providing twice as much
> hardware, then invoke mpiexec_mpt suitably to tell it to use all of
> that. Then, if you invoke mdrun_mpi the same way as you do now, it
> will work out it can use twice as much hardware per replica.
>
> Mark
>
> On Mon, Aug 5, 2013 at 7:55 AM, suhani nagpal <suhani.nagpal at gmail.com>
> wrote:
> > Greetings
> >
> > I'm running REMD of 96 replicas where the run.pbs is the following:
> >
> > #!/bin/tcsh
> > #PBS -S /bin/tcsh
> > #PBS -l walltime=00:15:00
> > #PBS -q workq
> > #PBS -l select=8:ncpus=12:mpiprocs=12
> > #PBS -l place=scatter:excl
> > #PBS -V
> >
> > # Go to the directory from which you submitted the job
> > cd $PBS_O_WORKDIR
> > setenv MPI_GROUP_MAX 1024
> > setenv MPI_UNBUFFERED_STDIO 1
> >
> > #mpiexec_mpt -np 24 ./exefile
> > mpiexec_mpt -np 96
> /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi
> > -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
> >
> >
> > So each replica runs at one processor.
> >
> > Now, I want to run the remd at 16 nodes ( double ) so that each replica
> is
> > subjected to 2 processors.
> >
> >
> > Kindly assist !
> >
> > Thanks
> > --
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