[gmx-users] Low cpu utilization

[Mark Abraham]

Hi,

As I said yesterday, you can't tell that about any program unless you look
at its output and how it performs with different amounts of resources.

Mark

On Mon, Oct 17, 2016 at 2:31 PM Mahmood Naderan <mahmood.nt at gmail.com>
wrote:

> Problem is that I can not find out if gromacs (or MPI) is using the
> resources correctly. Is there any idea to see if there is any bottleneck
> for such low utilization?
>
> Regards,
> Mahmood
>
>
>
> On Mon, Oct 17, 2016 at 11:30 AM, Mahmood Naderan <mahmood.nt at gmail.com>
> wrote:
>
> > it is interesting for me that I specified Verlet, but the log warns about
> > group.
> >
> > mahmood at cluster:LPN$ grep -r cut-off .
> > ./mdout.mdp:; cut-off scheme (group: using charge groups, Verlet:
> particle
> > based cut-offs)
> > ./mdout.mdp:; nblist cut-off
> > ./mdout.mdp:; long-range cut-off for switched potentials
> > ./mdout.mdp:; cut-off lengths
> > ./mdout.mdp:; Extension of the potential lookup tables beyond the cut-off
> > mahmood at cluster:LPN$ grep -r Verlet .
> > ./mdout.mdp:; cut-off scheme (group: using charge groups, Verlet:
> particle
> > based cut-offs)
> > ./mdout.mdp:cutoff-scheme            = Verlet
> > ./mdout.mdp:; Allowed energy drift due to the Verlet buffer in kJ/mol/ps
> > per atom,
> > ./mdout.mdp:coulomb-modifier         = Potential-shift-Verlet
> > ./mdout.mdp:vdw-modifier             = Potential-shift-Verlet
> >
> >
> >
> >
> > Regards,
> > Mahmood
> >
> --
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