[gmx-users] Running multiple Gromacs simulations on the same node

[MING HA]

Hi all,


Thanks for getting back to me so quickly. I found that when I did not
specify any
pinning, the running time of each simulation on the same node scaled
proportionally
to the number of concurrent Gromacs simulations. After some testing, i
found that
when I do not pin the core on which the simulations runs, then each Gromacs
simulations get mapped to the same process.

I have two questions:
1) Is the core on which the simulation runs pre-defined (e.g. each gromacs
simulation
starts on Core 0)?

2) Is there a way to tell Gromacs to allow the OS of the machine to
automatically schedule
different processes to run on different cores?


Thanks,
Ming

On Fri, Sep 8, 2017 at 9:07 AM, Szilárd Páll <pall.szilard at gmail.com> wrote:

> If you run MPI-enabled GROMACS and start N simulation with M(=1) ranks
> each, you will have N*M processes. That's how MPI works. However, you
> do not necessarily need to use MPI; the default build uses thread-MPI,
> for instance.
>
> --
> Szilárd
>
> On Fri, Sep 8, 2017 at 6:00 AM, MING HA <mingtha at scarletmail.rutgers.edu>
> wrote:
> > Hi all,
> >
> >
> > It may seem a bit weird, but I'm trying to run multiple Gromacs
> simulations
> > simultaneously on the same node, and I specified each Gromacs simulation
> > to use only 1 MPI process and 1 OMP thread. I'm doing this because I am
> > trying to check how accurate my model can predict an application using a
> > single thread and process.
> >
> > My question is: If, for example, I am running multiple Gromacs
> simulations
> > simultaneously, each with 1 MPI process and 1 OMP thread,  on the same
> > node, does each simulation use separate MPI processes and OMP threads,
> > or are they shared?
> >
> >
> > Sincerely,
> > Ming
> > --
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